1
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Sherwood M, Zhou Y, Sui Y, Wang Y, Skipp P, Kaid C, Gray J, Okamoto K, Ewing RM. Integrated re-analysis of transcriptomic and proteomic datasets reveals potential mechanisms for Zika viral-based oncolytic therapy in neuroblastoma. F1000Res 2024; 12:719. [PMID: 38903860 PMCID: PMC11187533 DOI: 10.12688/f1000research.132627.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/17/2024] [Indexed: 06/22/2024] Open
Abstract
Background Paediatric neuroblastoma and brain tumours account for a third of all childhood cancer-related mortality. High-risk neuroblastoma is highly aggressive and survival is poor despite intensive multi-modal therapies with significant toxicity. Novel therapies are desperately needed. The Zika virus (ZIKV) can access the nervous system and there is growing interest in employing ZIKV as a potential therapy against paediatric nervous system tumours, including neuroblastoma. Methods Here, we perform extensive data mining, integration and re-analysis of ZIKV infection datasets to highlight molecular mechanisms that may govern the oncolytic response in neuroblastoma cells. We collate infection data of multiple neuroblastoma cell lines by different ZIKV strains from a body of published literature to inform the susceptibility of neuroblastoma to the ZIKV oncolytic response. Integrating published transcriptomics, interaction proteomics, dependency factor and compound datasets we propose the involvement of multiple host systems during ZIKV infection. Results Through data mining of published literature, we observed most paediatric neuroblastoma cell lines to be highly susceptible to ZIKV infection and propose the PRVABC59 ZIKV strain to be the most promising candidate for neuroblastoma oncolytic virotherapy. ZIKV induces TNF signalling, lipid metabolism, the Unfolded Protein Response (UPR), and downregulates cell cycle and DNA replication processes. ZIKV infection is dependent on sterol regulatory element binding protein (SREBP)-regulated lipid metabolism and three protein complexes; V-ATPase, ER Membrane Protein Complex (EMC) and mammalian translocon. We propose ZIKV non-structural protein 4B (NS4B) as a likely mediator of ZIKVs interaction with IRE1-mediated UPR, lipid metabolism and mammalian translocon. Conclusions Our work provides a significant understanding of ZIKV infection in neuroblastoma cells, which will facilitate the progression of ZIKV-based oncolytic virotherapy through pre-clinical research and clinical trials.
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Affiliation(s)
- Matt Sherwood
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Yilu Zhou
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Yi Sui
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Yihua Wang
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Paul Skipp
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
| | - Carolini Kaid
- Human Genome and Stem-Cell Center (HUG-CELL), Biosciences Institute, Universidade de Sao Paulo, São Paulo, State of São Paulo, Brazil
| | - Juliet Gray
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, England, UK
| | - Keith Okamoto
- Human Genome and Stem-Cell Center (HUG-CELL), Biosciences Institute, Universidade de Sao Paulo, São Paulo, State of São Paulo, Brazil
| | - Rob M. Ewing
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, England, SO17 1BJ, UK
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2
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Ciucci G, Braga L, Zacchigna S. Discovery platforms for RNA therapeutics. Br J Pharmacol 2024. [PMID: 38760893 DOI: 10.1111/bph.16424] [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: 11/29/2023] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 05/20/2024] Open
Abstract
RNA therapeutics are emerging as a unique opportunity to drug currently "undruggable" molecules and diseases. While their advantages over conventional, small molecule drugs, their therapeutic implications and the tools for their effective in vivo delivery have been extensively reviewed, little attention has been so far paid to the technological platforms exploited for the discovery of RNA therapeutics. Here, we provide an overview of the existing platforms and ex vivo assays for RNA discovery, their advantages and disadvantages, as well as their main fields of application, with specific focus on RNA therapies that have reached either phase 3 or market approval.
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Affiliation(s)
- Giulio Ciucci
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Luca Braga
- Functional Cell Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Serena Zacchigna
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
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3
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Franks SN, Heon-Roberts R, Ryan BJ. CRISPRi: a way to integrate iPSC-derived neuronal models. Biochem Soc Trans 2024; 52:539-551. [PMID: 38526223 PMCID: PMC11088925 DOI: 10.1042/bst20230190] [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: 09/07/2023] [Revised: 02/28/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024]
Abstract
The genetic landscape of neurodegenerative diseases encompasses genes affecting multiple cellular pathways which exert effects in an array of neuronal and glial cell-types. Deconvolution of the roles of genes implicated in disease and the effects of disease-associated variants remains a vital step in the understanding of neurodegeneration and the development of therapeutics. Disease modelling using patient induced pluripotent stem cells (iPSCs) has enabled the generation of key cell-types associated with disease whilst maintaining the genomic variants that predispose to neurodegeneration. The use of CRISPR interference (CRISPRi), alongside other CRISPR-perturbations, allows the modelling of the effects of these disease-associated variants or identifying genes which modify disease phenotypes. This review summarises the current applications of CRISPRi in iPSC-derived neuronal models, such as fluorescence-activated cell sorting (FACS)-based screens, and discusses the future opportunities for disease modelling, identification of disease risk modifiers and target/drug discovery in neurodegeneration.
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Affiliation(s)
- Sarah N.J. Franks
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Rachel Heon-Roberts
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Brent J. Ryan
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
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4
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Tan WS, Rong E, Dry I, Lillico S, Law A, Digard P, Whitelaw B, Dalziel RG. Validation of Candidate Host Cell Entry Factors for Bovine Herpes Virus Type-1 Based on a Genome-Wide CRISPR Knockout Screen. Viruses 2024; 16:297. [PMID: 38400072 PMCID: PMC10893506 DOI: 10.3390/v16020297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
To identify host factors that affect Bovine Herpes Virus Type 1 (BoHV-1) infection we previously applied a genome wide CRISPR knockout screen targeting all bovine protein coding genes. By doing so we compiled a list of both pro-viral and anti-viral proteins involved in BoHV-1 replication. Here we provide further analysis of those that are potentially involved in viral entry into the host cell. We first generated single cell knockout clones deficient in some of the candidate genes for validation. We provide evidence that Polio Virus Receptor-related protein (PVRL2) serves as a receptor for BoHV-1, mediating more efficient entry than the previously identified Polio Virus Receptor (PVR). By knocking out two enzymes that catalyze HSPG chain elongation, HST2ST1 and GLCE, we further demonstrate the significance of HSPG in BoHV-1 entry. Another intriguing cluster of candidate genes, COG1, COG2 and COG4-7 encode six subunits of the Conserved Oligomeric Golgi (COG) complex. MDBK cells lacking COG6 produced fewer but bigger plaques compared to control cells, suggesting more efficient release of newly produced virions from these COG6 knockout cells, due to impaired HSPG biosynthesis. We further observed that viruses produced by the COG6 knockout cells consist of protein(s) with reduced N-glycosylation, potentially explaining their lower infectivity. To facilitate candidate validation, we also detailed a one-step multiplex CRISPR interference (CRISPRi) system, an orthogonal method to KO that enables quick and simultaneous deployment of three CRISPRs for efficient gene inactivation. Using CRISPR3i, we verified eight candidates that have been implicated in the synthesis of surface heparan sulfate proteoglycans (HSPGs). In summary, our experiments confirmed the two receptors PVR and PVRL2 for BoHV-1 entry into the host cell and other factors that affect this process, likely through the direct or indirect roles they play during HSPG synthesis and glycosylation of viral proteins.
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Affiliation(s)
- Wenfang Spring Tan
- Division of Infection and Immunity, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK (I.D.); (P.D.); (R.G.D.)
| | - Enguang Rong
- Division of Infection and Immunity, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK (I.D.); (P.D.); (R.G.D.)
| | - Inga Dry
- Division of Infection and Immunity, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK (I.D.); (P.D.); (R.G.D.)
| | - Simon Lillico
- Division of Functional Genetics and Development, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK; (S.L.); (B.W.)
- Centre for Tropical Livestock Genetics and Health, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK
| | - Andy Law
- Division of Genetics and Genomics, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK;
| | - Paul Digard
- Division of Infection and Immunity, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK (I.D.); (P.D.); (R.G.D.)
| | - Bruce Whitelaw
- Division of Functional Genetics and Development, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK; (S.L.); (B.W.)
- Division of Genetics and Genomics, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK;
| | - Robert G. Dalziel
- Division of Infection and Immunity, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh EH259RG, UK (I.D.); (P.D.); (R.G.D.)
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5
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Beirute-Herrera J, López-Amo Calvo B, Edenhofer F, Esk C. The promise of genetic screens in human in vitro brain models. Biol Chem 2024; 405:13-24. [PMID: 37697643 DOI: 10.1515/hsz-2023-0174] [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: 04/04/2023] [Accepted: 08/21/2023] [Indexed: 09/13/2023]
Abstract
Advances of in vitro culture models have allowed unprecedented insights into human neurobiology. At the same time genetic screening has matured into a robust and accessible experimental strategy allowing for the simultaneous study of many genes in parallel. The combination of both technologies is a newly emerging tool for neuroscientists, opening the door to identifying causal cell- and tissue-specific developmental and disease mechanisms. However, with complex experimental genetic screening set-ups new challenges in data interpretation and experimental scope arise that require a deep understanding of the benefits and challenges of individual approaches. In this review, we summarize the literature that applies genetic screening to in vitro brain models, compare experimental strengths and weaknesses and point towards future directions of these promising approaches.
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Affiliation(s)
- Julianne Beirute-Herrera
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Beatriz López-Amo Calvo
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Frank Edenhofer
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Christopher Esk
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
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6
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Wang WX, Douglas TR, Zhang H, Bhattacharya A, Rothenbroker M, Tang W, Sun Y, Jia Z, Muffat J, Li Y, Chou LYT. Universal, label-free, single-molecule visualization of DNA origami nanodevices across biological samples using origamiFISH. NATURE NANOTECHNOLOGY 2024; 19:58-69. [PMID: 37500778 DOI: 10.1038/s41565-023-01449-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 06/09/2023] [Indexed: 07/29/2023]
Abstract
Structural DNA nanotechnology enables the fabrication of user-defined DNA origami nanostructures (DNs) for biological applications. However, the role of DN design during cellular interactions and subsequent biodistribution remain poorly understood. Current methods for tracking DN fates in situ, including fluorescent-dye labelling, suffer from low sensitivity and dye-induced artifacts. Here we present origamiFISH, a label-free and universal method for the single-molecule fluorescence detection of DNA origami nanostructures in cells and tissues. origamiFISH targets pan-DN scaffold sequences with hybridization chain reaction probes to achieve 1,000-fold signal amplification. We identify cell-type- and DN shape-specific spatiotemporal distribution patterns within a minute of uptake and at picomolar DN concentrations, 10,000× lower than field standards. We additionally optimize compatibility with immunofluorescence and tissue clearing to visualize DN distribution within tissue cryo-/vibratome sections, slice cultures and whole-mount organoids. Together, origamiFISH enables the accurate mapping of DN distribution across subcellular and tissue barriers for guiding the development of DN-based therapeutics.
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Affiliation(s)
- Wendy Xueyi Wang
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Travis R Douglas
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Haiwang Zhang
- Department of Neurosurgery, Guizhou Provincial People's Hospital, Guiyang, China
- Program in Neurosciences and Mental Health, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Afrin Bhattacharya
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Meghan Rothenbroker
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Wentian Tang
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Yu Sun
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Zhengping Jia
- Program in Neurosciences and Mental Health, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Julien Muffat
- Program in Neurosciences and Mental Health, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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7
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Tan WS, Rong E, Dry I, Lillico SG, Law A, Digard P, Whitelaw B, Dalziel RG. GARP and EARP are required for efficient BoHV-1 replication as identified by a genome wide CRISPR knockout screen. PLoS Pathog 2023; 19:e1011822. [PMID: 38055775 PMCID: PMC10727446 DOI: 10.1371/journal.ppat.1011822] [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: 11/27/2022] [Revised: 12/18/2023] [Accepted: 11/13/2023] [Indexed: 12/08/2023] Open
Abstract
The advances in gene editing bring unprecedented opportunities in high throughput functional genomics to animal research. Here we describe a genome wide CRISPR knockout library, btCRISPRko.v1, targeting all protein coding genes in the cattle genome. Using it, we conducted genome wide screens during Bovine Herpes Virus type 1 (BoHV-1) replication and compiled a list of pro-viral and anti-viral candidates. These candidates might influence multiple aspects of BoHV-1 biology such as viral entry, genome replication and transcription, viral protein trafficking and virion maturation in the cytoplasm. Some of the most intriguing examples are VPS51, VPS52 and VPS53 that code for subunits of two membrane tethering complexes, the endosome-associated recycling protein (EARP) complex and the Golgi-associated retrograde protein (GARP) complex. These complexes mediate endosomal recycling and retrograde trafficking to the trans Golgi Network (TGN). Simultaneous loss of both complexes in MDBKs resulted in greatly reduced production of infectious BoHV-1 virions. We also found that viruses released by these deficient cells severely lack VP8, the most abundant tegument protein of BoHV-1 that are crucial for its virulence. In combination with previous reports, our data suggest vital roles GARP and EARP play during viral protein packaging and capsid re-envelopment in the cytoplasm. It also contributes to evidence that both the TGN and the recycling endosomes are recruited in this process, mediated by these complexes. The btCRISPRko.v1 library generated here has been controlled for quality and shown to be effective in host gene discovery. We hope it will facilitate efforts in the study of other pathogens and various aspects of cell biology in cattle.
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Affiliation(s)
- Wenfang S. Tan
- Division of Infection and Immunity, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Enguang Rong
- Division of Infection and Immunity, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Inga Dry
- Division of Infection and Immunity, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Simon G. Lillico
- Division of Functional Genetics and Development, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Centre for Tropical Livestock Genetics and Health, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Andy Law
- Division of Genetics and Genomics, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Paul Digard
- Division of Infection and Immunity, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Bruce Whitelaw
- Division of Functional Genetics and Development, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Centre for Tropical Livestock Genetics and Health, the Roslin Institute, Easter Bush Campus, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Robert G. Dalziel
- Division of Infection and Immunity, University of Edinburgh, Edinburgh, Scotland, United Kingdom
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8
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Ramezannia Z, Shamekh A, Bannazadeh Baghi H. CRISPR-Cas system to discover host-virus interactions in Flaviviridae. Virol J 2023; 20:247. [PMID: 37891676 PMCID: PMC10605781 DOI: 10.1186/s12985-023-02216-7] [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: 03/10/2023] [Accepted: 10/25/2023] [Indexed: 10/29/2023] Open
Abstract
The Flaviviridae virus family members cause severe human diseases and are responsible for considerable mortality and morbidity worldwide. Therefore, researchers have conducted genetic screens to enhance insight into viral dependency and develop potential anti-viral strategies to treat and prevent these infections. The host factors identified by the clustered regularly interspaced short palindromic repeats (CRISPR) system can be potential targets for drug development. Meanwhile, CRISPR technology can be efficiently used to treat viral diseases as it targets both DNA and RNA. This paper discusses the host factors related to the life cycle of viruses of this family that were recently discovered using the CRISPR system. It also explores the role of immune factors and recent advances in gene editing in treating flavivirus-related diseases. The ever-increasing advancements of this technology may promise new therapeutic approaches with unique capabilities, surpassing the traditional methods of drug production and treatment.
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Affiliation(s)
- Zahra Ramezannia
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Virology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ali Shamekh
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 5166/15731, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 5166/15731, Iran.
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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9
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Srivastava K, Pandit B. Genome-wide CRISPR screens and their applications in infectious disease. Front Genome Ed 2023; 5:1243731. [PMID: 37794981 PMCID: PMC10546192 DOI: 10.3389/fgeed.2023.1243731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023] Open
Abstract
Inactivation or targeted disruption of a gene provides clues to assess the function of the gene in many cellular processes. Knockdown or knocking out a gene has been widely used for this purpose. However, recently CRISPR mediated genome editing has taken over the knockout/knockdown system with more precision. CRISPR technique has enabled us to perform targeted mutagenesis or genome editing to address questions in fundamental biology to biomedical research. Its application is wide in understanding the role of genes in the disease process, and response to therapy in cancer, metabolic disorders, or infectious disease. In this article, we have focused on infectious disease and how genome-wide CRISPR screens have enabled us to identify host factors involved in the process of infection. Understanding the biology of the host-pathogen interaction is of immense importance in planning host-directed therapy to improve better management of the disease. Genome-wide CRISPR screens provide strong mechanistic ways to identify the host dependency factors involved in various infections. We presented insights into genome-wide CRISPR screens conducted in the context of infectious diseases both viral and bacterial that led to better understanding of host-pathogen interactions and immune networks. We have discussed the advancement of knowledge pertaining to influenza virus, different hepatitis viruses, HIV, most recent SARS CoV2 and few more. Among bacterial diseases, we have focused on infection with life threatening Mycobacteria, Salmonella, S. aureus, etc. It appears that the CRISPR technique can be applied universally to multiple infectious disease models to unravel the role of known or novel host factors.
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Affiliation(s)
| | - Bhaswati Pandit
- National Institute of Biomedical Genomics (NIBMG), Calcutta, West Bengal, India
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10
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Balmas E, Sozza F, Bottini S, Ratto ML, Savorè G, Becca S, Snijders KE, Bertero A. Manipulating and studying gene function in human pluripotent stem cell models. FEBS Lett 2023; 597:2250-2287. [PMID: 37519013 DOI: 10.1002/1873-3468.14709] [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: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are uniquely suited to study human development and disease and promise to revolutionize regenerative medicine. These applications rely on robust methods to manipulate gene function in hPSC models. This comprehensive review aims to both empower scientists approaching the field and update experienced stem cell biologists. We begin by highlighting challenges with manipulating gene expression in hPSCs and their differentiated derivatives, and relevant solutions (transfection, transduction, transposition, and genomic safe harbor editing). We then outline how to perform robust constitutive or inducible loss-, gain-, and change-of-function experiments in hPSCs models, both using historical methods (RNA interference, transgenesis, and homologous recombination) and modern programmable nucleases (particularly CRISPR/Cas9 and its derivatives, i.e., CRISPR interference, activation, base editing, and prime editing). We further describe extension of these approaches for arrayed or pooled functional studies, including emerging single-cell genomic methods, and the related design and analytical bioinformatic tools. Finally, we suggest some directions for future advancements in all of these areas. Mastering the combination of these transformative technologies will empower unprecedented advances in human biology and medicine.
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Affiliation(s)
- Elisa Balmas
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Federica Sozza
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Sveva Bottini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Maria Luisa Ratto
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Giulia Savorè
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Silvia Becca
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Kirsten Esmee Snijders
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Alessandro Bertero
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
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11
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Shevade K, Peddada S, Mader K, Przybyla L. Functional genomics in stem cell models: considerations and applications. Front Cell Dev Biol 2023; 11:1236553. [PMID: 37554308 PMCID: PMC10404852 DOI: 10.3389/fcell.2023.1236553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023] Open
Abstract
Protocols to differentiate human pluripotent stem cells have advanced in terms of cell type specificity and tissue-level complexity over the past 2 decades, which has facilitated human disease modeling in the most relevant cell types. The ability to generate induced PSCs (iPSCs) from patients further enables the study of disease mutations in an appropriate cellular context to reveal the mechanisms that underlie disease etiology and progression. As iPSC-derived disease models have improved in robustness and scale, they have also been adopted more widely for use in drug screens to discover new therapies and therapeutic targets. Advancement in genome editing technologies, in particular the discovery of CRISPR-Cas9, has further allowed for rapid development of iPSCs containing disease-causing mutations. CRISPR-Cas9 technologies have now evolved beyond creating single gene edits, aided by the fusion of inhibitory (CRISPRi) or activation (CRISPRa) domains to a catalytically dead Cas9 protein, enabling inhibition or activation of endogenous gene loci. These tools have been used in CRISPR knockout, CRISPRi, or CRISPRa screens to identify genetic modifiers that synergize or antagonize with disease mutations in a systematic and unbiased manner, resulting in identification of disease mechanisms and discovery of new therapeutic targets to accelerate drug discovery research. However, many technical challenges remain when applying large-scale functional genomics approaches to differentiated PSC populations. Here we review current technologies in the field of iPSC disease modeling and CRISPR-based functional genomics screens and practical considerations for implementation across a range of modalities, applications, and disease areas, as well as explore CRISPR screens that have been performed in iPSC models to-date and the insights and therapies these screens have produced.
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Affiliation(s)
- Kaivalya Shevade
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Sailaja Peddada
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Karl Mader
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Laralynne Przybyla
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
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12
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Seok Y, Mauk MG, Li R, Qian C. Trends of respiratory virus detection in point-of-care testing: A review. Anal Chim Acta 2023; 1264:341283. [PMID: 37230728 DOI: 10.1016/j.aca.2023.341283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
In resource-limited conditions such as the COVID-19 pandemic, on-site detection of diseases using the Point-of-care testing (POCT) technique is becoming a key factor in overcoming crises and saving lives. For practical POCT in the field, affordable, sensitive, and rapid medical testing should be performed on simple and portable platforms, instead of laboratory facilities. In this review, we introduce recent approaches to the detection of respiratory virus targets, analysis trends, and prospects. Respiratory viruses occur everywhere and are one of the most common and widely spreading infectious diseases in the human global society. Seasonal influenza, avian influenza, coronavirus, and COVID-19 are examples of such diseases. On-site detection and POCT for respiratory viruses are state-of-the-art technologies in this field and are commercially valuable global healthcare topics. Cutting-edge POCT techniques have focused on the detection of respiratory viruses for early diagnosis, prevention, and monitoring to protect against the spread of COVID-19. In particular, we highlight the application of sensing techniques to each platform to reveal the challenges of the development stage. Recent POCT approaches have been summarized in terms of principle, sensitivity, analysis time, and convenience for field applications. Based on the analysis of current states, we also suggest the remaining challenges and prospects for the use of the POCT technique for respiratory virus detection to improve our protection ability and prevent the next pandemic.
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Affiliation(s)
- Youngung Seok
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju, 61186, Republic of Korea; Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, 216 Towne Building, 220 S. 33rd Street, Philadelphia, PA, 19104, USA.
| | - Michael G Mauk
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, 216 Towne Building, 220 S. 33rd Street, Philadelphia, PA, 19104, USA
| | - Ruijie Li
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 29 Zhongguancun East Road, Haidian District, Beijing, 100190, China
| | - Cheng Qian
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, China
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13
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Li K, Ouyang M, Zhan J, Tian R. CRISPR-based functional genomics screening in human-pluripotent-stem-cell-derived cell types. CELL GENOMICS 2023; 3:100300. [PMID: 37228745 PMCID: PMC10203043 DOI: 10.1016/j.xgen.2023.100300] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
While our knowledge of gene expression in different human cell types is rapidly expanding with advances in transcriptomic profiling technologies, the next challenge is to understand gene function in each cell type. CRISPR-Cas9-based functional genomics screening offers a powerful approach to determine gene function in a high-throughput manner. With the maturation of stem cell technology, a variety of human cell types can be derived from human pluripotent stem cells (hPSCs). Recently, the integration of CRISPR screening with hPSC differentiation technologies opens up unprecedented opportunities to systematically examine gene function in different human cell types and identify mechanisms and therapeutic targets for human diseases. This review highlights recent progress in the development and applications of CRISPR-Cas9-based functional genomics screening in hPSC-derived cell types, discusses current challenges and limitations, and outlines future directions for this emerging field.
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Affiliation(s)
- Kun Li
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Miao Ouyang
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Jiangshan Zhan
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Ruilin Tian
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
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14
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Ohlson MB, Eitson JL, Wells AI, Kumar A, Jang S, Ni C, Xing C, Buszczak M, Schoggins JW. Genome-Scale CRISPR Screening Reveals Host Factors Required for Ribosome Formation and Viral Replication. mBio 2023; 14:e0012723. [PMID: 36809113 PMCID: PMC10128003 DOI: 10.1128/mbio.00127-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 02/23/2023] Open
Abstract
Viruses are known to co-opt host machinery for translation initiation, but less is known about which host factors are required for the formation of ribosomes used to synthesize viral proteins. Using a loss-of-function CRISPR screen, we show that synthesis of a flavivirus-encoded fluorescent reporter depends on multiple host factors, including several 60S ribosome biogenesis proteins. Viral phenotyping revealed that two of these factors, SBDS, a known ribosome biogenesis factor, and the relatively uncharacterized protein SPATA5, were broadly required for replication of flaviviruses, coronaviruses, alphaviruses, paramyxoviruses, an enterovirus, and a poxvirus. Mechanistic studies revealed that loss of SPATA5 caused defects in rRNA processing and ribosome assembly, suggesting that this human protein may be a functional ortholog of yeast Drg1. These studies implicate specific ribosome biogenesis proteins as viral host dependency factors that are required for synthesis of virally encoded protein and accordingly, optimal viral replication. IMPORTANCE Viruses are well known for their ability to co-opt host ribosomes to synthesize viral proteins. The specific factors involved in translation of viral RNAs are not fully described. In this study, we implemented a unique genome-scale CRISPR screen to identify previously uncharacterized host factors that are important for the synthesis of virally encoded protein. We found that multiple genes involved in 60S ribosome biogenesis were required for viral RNA translation. Loss of these factors severely impaired viral replication. Mechanistic studies on the AAA ATPase SPATA5 indicate that this host factor is required for a late step in ribosome formation. These findings reveal insight into the identity and function of specific ribosome biogenesis proteins that are critical for viral infections.
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Affiliation(s)
- Maikke B. Ohlson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jennifer L. Eitson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Alexandra I. Wells
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Seoyeon Jang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Chunyang Ni
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - John W. Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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15
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Carlson RJ, Leiken MD, Guna A, Hacohen N, Blainey PC. A genome-wide optical pooled screen reveals regulators of cellular antiviral responses. Proc Natl Acad Sci U S A 2023; 120:e2210623120. [PMID: 37043539 PMCID: PMC10120039 DOI: 10.1073/pnas.2210623120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/06/2023] [Indexed: 04/13/2023] Open
Abstract
The infection of mammalian cells by viruses and innate immune responses to infection are spatiotemporally organized processes. Cytosolic RNA sensors trigger nuclear translocation of the transcription factor interferon regulatory factor 3 (IRF3) and consequent induction of host immune responses to RNA viruses. Previous genetic screens for factors involved in viral sensing did not resolve changes in the subcellular localization of host or viral proteins. Here, we increased the throughput of our optical pooled screening technology by over fourfold. This allowed us to carry out a genome-wide CRISPR knockout screen using high-resolution multiparameter imaging of cellular responses to Sendai virus infection coupled with in situ cDNA sequencing by synthesis (SBS) to identify 80,408 single guide RNAs (sgRNAs) in 10,366,390 cells-over an order of magnitude more genomic perturbations than demonstrated previously using an in situ SBS readout. By ranking perturbations using human-designed and deep learning image feature scores, we identified regulators of IRF3 translocation, Sendai virus localization, and peroxisomal biogenesis. Among the hits, we found that ATP13A1, an ER-localized P5A-type ATPase, is essential for viral sensing and is required for targeting of mitochondrial antiviral signaling protein (MAVS) to mitochondrial membranes where MAVS must be localized for effective signaling through retinoic acid-inducible gene I (RIG-I). The ability to carry out genome-wide pooled screens with complex high-resolution image-based phenotyping dramatically expands the scope of functional genomics approaches.
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Affiliation(s)
- Rebecca J. Carlson
- Department of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA02139
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
| | - Michael D. Leiken
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
| | | | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA02114
| | - Paul C. Blainey
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA02139
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16
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Kulkarni V, Jayakumar S, Mohan M, Kulkarni S. Aid or Antagonize: Nuclear Long Noncoding RNAs Regulate Host Responses and Outcomes of Viral Infections. Cells 2023; 12:987. [PMID: 37048060 PMCID: PMC10093752 DOI: 10.3390/cells12070987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts measuring >200 bp in length and devoid of protein-coding potential. LncRNAs exceed the number of protein-coding mRNAs and regulate cellular, developmental, and immune pathways through diverse molecular mechanisms. In recent years, lncRNAs have emerged as epigenetic regulators with prominent roles in health and disease. Many lncRNAs, either host or virus-encoded, have been implicated in critical cellular defense processes, such as cytokine and antiviral gene expression, the regulation of cell signaling pathways, and the activation of transcription factors. In addition, cellular and viral lncRNAs regulate virus gene expression. Viral infections and associated immune responses alter the expression of host lncRNAs regulating immune responses, host metabolism, and viral replication. The influence of lncRNAs on the pathogenesis and outcomes of viral infections is being widely explored because virus-induced lncRNAs can serve as diagnostic and therapeutic targets. Future studies should focus on thoroughly characterizing lncRNA expressions in virus-infected primary cells, investigating their role in disease prognosis, and developing biologically relevant animal or organoid models to determine their suitability for specific therapeutic targeting. Many cellular and viral lncRNAs localize in the nucleus and epigenetically modulate viral transcription, latency, and host responses to infection. In this review, we provide an overview of the role of nuclear lncRNAs in the pathogenesis and outcomes of viral infections, such as the Influenza A virus, Sendai Virus, Respiratory Syncytial Virus, Hepatitis C virus, Human Immunodeficiency Virus, and Herpes Simplex Virus. We also address significant advances and barriers in characterizing lncRNA function and explore the potential of lncRNAs as therapeutic targets.
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Affiliation(s)
- Viraj Kulkarni
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
| | - Sahana Jayakumar
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Mahesh Mohan
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Smita Kulkarni
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
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17
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Wells MF, Nemesh J, Ghosh S, Mitchell JM, Salick MR, Mello CJ, Meyer D, Pietilainen O, Piccioni F, Guss EJ, Raghunathan K, Tegtmeyer M, Hawes D, Neumann A, Worringer KA, Ho D, Kommineni S, Chan K, Peterson BK, Raymond JJ, Gold JT, Siekmann MT, Zuccaro E, Nehme R, Kaykas A, Eggan K, McCarroll SA. Natural variation in gene expression and viral susceptibility revealed by neural progenitor cell villages. Cell Stem Cell 2023; 30:312-332.e13. [PMID: 36796362 PMCID: PMC10581885 DOI: 10.1016/j.stem.2023.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/28/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023]
Abstract
Human genome variation contributes to diversity in neurodevelopmental outcomes and vulnerabilities; recognizing the underlying molecular and cellular mechanisms will require scalable approaches. Here, we describe a "cell village" experimental platform we used to analyze genetic, molecular, and phenotypic heterogeneity across neural progenitor cells from 44 human donors cultured in a shared in vitro environment using algorithms (Dropulation and Census-seq) to assign cells and phenotypes to individual donors. Through rapid induction of human stem cell-derived neural progenitor cells, measurements of natural genetic variation, and CRISPR-Cas9 genetic perturbations, we identified a common variant that regulates antiviral IFITM3 expression and explains most inter-individual variation in susceptibility to the Zika virus. We also detected expression QTLs corresponding to GWAS loci for brain traits and discovered novel disease-relevant regulators of progenitor proliferation and differentiation such as CACHD1. This approach provides scalable ways to elucidate the effects of genes and genetic variation on cellular phenotypes.
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Affiliation(s)
- Michael F Wells
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James Nemesh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jana M Mitchell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Insitro, South San Francisco, CA 94080, USA
| | | | - Curtis J Mello
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Olli Pietilainen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Federica Piccioni
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Ellen J Guss
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kavya Raghunathan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Derek Hawes
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Anna Neumann
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Kathleen A Worringer
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Daniel Ho
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Sravya Kommineni
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Karrie Chan
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Brant K Peterson
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Joseph J Raymond
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - John T Gold
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Biology, Davidson College, Davidson, NC 28035, USA
| | - Marco T Siekmann
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Emanuela Zuccaro
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | | | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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18
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Pandemic city: Village-in-a-dish unlocks dynamic genetic effects in the brain. Cell Stem Cell 2023; 30:239-241. [PMID: 36868190 DOI: 10.1016/j.stem.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
In this issue, Wells et al. combine genetic multiplexing ("village-in-a-dish") and Stem-cell-derived NGN2-accelerated Progenitors (SNaPs) to evaluate genotype-phenotype relationships across 100 donors in the context of Zika virus infection in the developing brain. This resource will be broadly applicable in uncovering how genetic variation underlies risk for neurodevelopmental disorders.
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19
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Ahmed M, Muffat J, Li Y. Understanding neural development and diseases using CRISPR screens in human pluripotent stem cell-derived cultures. Front Cell Dev Biol 2023; 11:1158373. [PMID: 37101616 PMCID: PMC10123288 DOI: 10.3389/fcell.2023.1158373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/30/2023] [Indexed: 04/28/2023] Open
Abstract
The brain is arguably the most complex part of the human body in form and function. Much remains unclear about the molecular mechanisms that regulate its normal and pathological physiology. This lack of knowledge largely stems from the inaccessible nature of the human brain, and the limitation of animal models. As a result, brain disorders are difficult to understand and even more difficult to treat. Recent advances in generating human pluripotent stem cells (hPSCs)-derived 2-dimensional (2D) and 3-dimensional (3D) neural cultures have provided an accessible system to model the human brain. Breakthroughs in gene editing technologies such as CRISPR/Cas9 further elevate the hPSCs into a genetically tractable experimental system. Powerful genetic screens, previously reserved for model organisms and transformed cell lines, can now be performed in human neural cells. Combined with the rapidly expanding single-cell genomics toolkit, these technological advances culminate to create an unprecedented opportunity to study the human brain using functional genomics. This review will summarize the current progress of applying CRISPR-based genetic screens in hPSCs-derived 2D neural cultures and 3D brain organoids. We will also evaluate the key technologies involved and discuss their related experimental considerations and future applications.
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Affiliation(s)
- Mai Ahmed
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Julien Muffat
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Yun Li,
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20
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Paiva IM, Damasceno S, Cunha TM. CRISPR Libraries and Whole-Genome Screening to Identify Essential Factors for Viral Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1429:157-172. [PMID: 37486521 DOI: 10.1007/978-3-031-33325-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The CRISPR-Cas9 system has revolutionized genetics and offers a simple and inexpensive way of generating perturbation that results in gene repression, activation, or editing. The advances in this technique make possible the development of CRISPR libraries which consist of a set of sgRNAs to cause perturbations in several genes in the same cell population. The use of libraries raised the CRISPR-Cas9 technique to a genomic scale and provides a powerful approach for identifying previously unknown molecular mechanisms and pathways involved in a specific phenotype or biological process. More specifically, the CRISPRko libraries (set of sgRNAs for gene knockout) and their high-throughput screenings are widely used in research with viral agents, and it was enlarged even more with the COVID-19 pandemic. With this chapter, we aim to point out how this tool helps in understanding virus-host relationships, such as the mechanisms of virus entry into the cell, the essential factors for its replication, and the cellular pathways involved in the response against the pathogen. The chapter also provided some practical considerations for each step of an experimentation using these tools that include choosing the library and screening type, the target cell, the viral strain, the library amplification and guaranteeing its coverage, the strategies for the gene screening pipeline by bioinformatics, and finally, target validation. To conclude, it was presented a table reviewing the last updates in the research for antiviral therapies using CRISPR libraries.
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Affiliation(s)
- Isadora Marques Paiva
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, SP, Brazil
| | - Samara Damasceno
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, SP, Brazil
| | - Thiago Mattar Cunha
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, SP, Brazil.
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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21
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Matía A, Lorenzo MM, Romero-Estremera YC, Sánchez-Puig JM, Zaballos A, Blasco R. Identification of β2 microglobulin, the product of B2M gene, as a Host Factor for Vaccinia Virus Infection by Genome-Wide CRISPR genetic screens. PLoS Pathog 2022; 18:e1010800. [PMID: 36574441 PMCID: PMC9829182 DOI: 10.1371/journal.ppat.1010800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 01/09/2023] [Accepted: 12/13/2022] [Indexed: 12/28/2022] Open
Abstract
Genome-wide genetic screens are powerful tools to identify genes that act as host factors of viruses. We have applied this technique to analyze the infection of HeLa cells by Vaccinia virus, in an attempt to find genes necessary for infection. Infection of cell populations harboring single gene inactivations resulted in no surviving cells, suggesting that no single gene knock-out was able to provide complete resistance to Vaccinia virus and thus allow cells to survive infection. In the absence of an absolute infection blockage, we explored if some gene inactivations could provide partial protection leading to a reduced probability of infection. Multiple experiments using modified screening procedures involving replication restricted viruses led to the identification of multiple genes whose inactivation potentially increase resistance to infection and therefore cell survival. As expected, significant gene hits were related to proteins known to act in virus entry, such as ITGB1 and AXL as well as genes belonging to their downstream related pathways. Additionally, we consistently found β2-microglobulin, encoded by the B2M gene, among the screening top hits, a novel finding that was further explored. Inactivation of B2M resulted in 54% and 91% reduced VV infection efficiency in HeLa and HAP1 cell lines respectively. In the absence of B2M, while virus binding to the cells was unaffected, virus internalization and early gene expression were significantly diminished. These results point to β2-microglobulin as a relevant factor in the Vaccinia virus entry process.
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Affiliation(s)
- Alejandro Matía
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria–Consejo Superior de Investigaciones Científicas (INIA–CSIC), Madrid, Spain
| | - Maria M. Lorenzo
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria–Consejo Superior de Investigaciones Científicas (INIA–CSIC), Madrid, Spain
| | - Yolimar C. Romero-Estremera
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria–Consejo Superior de Investigaciones Científicas (INIA–CSIC), Madrid, Spain
| | - Juana M. Sánchez-Puig
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria–Consejo Superior de Investigaciones Científicas (INIA–CSIC), Madrid, Spain
| | - Angel Zaballos
- Unidad de Genómica, Centro Nacional de Microbiología-ISCIII, Madrid, Spain
| | - Rafael Blasco
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria–Consejo Superior de Investigaciones Científicas (INIA–CSIC), Madrid, Spain
- * E-mail:
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22
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Towards elucidating disease-relevant states of neurons and glia by CRISPR-based functional genomics. Genome Med 2022; 14:130. [PMID: 36401300 PMCID: PMC9673433 DOI: 10.1186/s13073-022-01134-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
Our understanding of neurological diseases has been tremendously enhanced over the past decade by the application of new technologies. Genome-wide association studies have highlighted glial cells as important players in diseases. Single-cell profiling technologies are providing descriptions of disease states of neurons and glia at unprecedented molecular resolution. However, significant gaps remain in our understanding of the mechanisms driving disease-associated cell states, and how these states contribute to disease. These gaps in our understanding can be bridged by CRISPR-based functional genomics, a powerful approach to systematically interrogate gene function. In this review, we will briefly review the current literature on neurological disease-associated cell states and introduce CRISPR-based functional genomics. We discuss how advances in CRISPR-based screens, especially when implemented in the relevant brain cell types or cellular environments, have paved the way towards uncovering mechanisms underlying neurological disease-associated cell states. Finally, we will delineate current challenges and future directions for CRISPR-based functional genomics to further our understanding of neurological diseases and potential therapeutic strategies.
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Yang X, Zhao X, Zhu Y, Xun J, Wen Q, Pan H, Yang J, Wang J, Liang Z, Shen X, Liang Y, Lin Q, Liang H, Li M, Chen J, Jiang S, Xu J, Lu H, Zhu H. FBXO34 promotes latent HIV-1 activation by post-transcriptional modulation. Emerg Microbes Infect 2022; 11:2785-2799. [PMID: 36285453 PMCID: PMC9665091 DOI: 10.1080/22221751.2022.2140605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Acquired immunodeficiency syndrome (AIDS) cannot be completely cured, mainly due to the existence of a latent HIV-1 reservoir. However, our current understanding of the molecular mechanisms underlying the establishment and maintenance of HIV-1 latent reservoir is not comprehensive. Here, using a genome-wide CRISPR-Cas9 activation library screening, we identified E3 ubiquitin ligase F-box protein 34 (FBXO34) and the substrate of FBXO34, heterogeneous nuclear ribonucleoprotein U (hnRNP U) was identified by affinity purification mass spectrometry, as new host factors related to HIV-1 latent maintenance. Overexpression of FBXO34 or knockout of hnRNP U can activate latent HIV-1 in multiple latent cell lines. FBXO34 mainly promotes hnRNP U ubiquitination, which leads to hnRNP U degradation and abolishment of the interaction between hnRNP U and HIV-1 mRNA. In a latently infected cell line, hnRNP U interacts with the ReV region of HIV-1 mRNA through amino acids 1-339 to hinder HIV-1 translation, thereby, promoting HIV-1 latency. Importantly, we confirmed the role of the FBXO34/hnRNP U axis in the primary CD4+ T lymphocyte model, and detected differences in hnRNP U expression levels in samples from patients treated with antiretroviral therapy (ART) and healthy people, which further suggests that the FBXO34/hnRNP U axis is a new pathway involved in HIV-1 latency. These results provide mechanistic insights into the critical role of ubiquitination and hnRNP U in HIV-1 latency. This novel FBXO34/hnRNP U axis in HIV transcription may be directly targeted to control HIV reservoirs in patients in the future.
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Affiliation(s)
- Xinyi Yang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaying Zhao
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuqi Zhu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jingna Xun
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qin Wen
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hanyu Pan
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinlong Yang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jing Wang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhimin Liang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaoting Shen
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yue Liang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qinru Lin
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Huitong Liang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Min Li
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jun Chen
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shibo Jiang
- Department of Infectious Disease, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jianqing Xu
- Department of Infectious Disease, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hongzhou Lu
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Huanzhang Zhu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
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Flavivirus-Host Interaction Landscape Visualized through Genome-Wide CRISPR Screens. Viruses 2022; 14:v14102164. [PMID: 36298718 PMCID: PMC9609550 DOI: 10.3390/v14102164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/25/2022] [Accepted: 09/25/2022] [Indexed: 11/14/2022] Open
Abstract
Flaviviruses comprise several important human pathogens which cause significant morbidity and mortality worldwide. Like any other virus, they are obligate intracellular parasites. Therefore, studying the host cellular factors that promote or restrict their replication and pathogenesis becomes vital. Since inhibiting the host dependency factors or activating the host restriction factors can suppress the viral replication and propagation in the cell, identifying them reveals potential targets for antiviral therapeutics. Clustered regularly interspaced short palindromic repeats (CRISPR) technology has provided an effective means of producing customizable genetic modifications and performing forward genetic screens in a broad spectrum of cell types and organisms. The ease, rapidity, and high reproducibility of CRISPR technology have made it an excellent tool for carrying out genome-wide screens to identify and characterize viral host dependency factors systematically. Here, we review the insights from various Genome-wide CRISPR screens that have advanced our understanding of Flavivirus-Host interactions.
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LaNoce E, Dumeng-Rodriguez J, Christian KM. Using 2D and 3D pluripotent stem cell models to study neurotropic viruses. FRONTIERS IN VIROLOGY 2022; 2:869657. [PMID: 36325520 PMCID: PMC9624474 DOI: 10.3389/fviro.2022.869657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Understanding the impact of viral pathogens on the human central nervous system (CNS) has been challenging due to the lack of viable human CNS models for controlled experiments to determine the causal factors underlying pathogenesis. Human embryonic stem cells (ESCs) and, more recently, cellular reprogramming of adult somatic cells to generate human induced pluripotent stem cells (iPSCs) provide opportunities for directed differentiation to neural cells that can be used to evaluate the impact of known and emerging viruses on neural cell types. Pluripotent stem cells (PSCs) can be induced to neural lineages in either two- (2D) or three-dimensional (3D) cultures, each bearing distinct advantages and limitations for modeling viral pathogenesis and evaluating effective therapeutics. Here we review the current state of technology in stem cell-based modeling of the CNS and how these models can be used to determine viral tropism and identify cellular phenotypes to investigate virus-host interactions and facilitate drug screening. We focus on several viruses (e.g., human immunodeficiency virus (HIV), herpes simplex virus (HSV), Zika virus (ZIKV), human cytomegalovirus (HCMV), SARS-CoV-2, West Nile virus (WNV)) to illustrate key advantages, as well as challenges, of PSC-based models. We also discuss how human PSC-based models can be used to evaluate the safety and efficacy of therapeutic drugs by generating data that are complementary to existing preclinical models. Ultimately, these efforts could facilitate the movement towards personalized medicine and provide patients and physicians with an additional source of information to consider when evaluating available treatment strategies.
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Affiliation(s)
- Emma LaNoce
- Mahoney Institute for Neurosciences, Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jeriel Dumeng-Rodriguez
- Developmental, Stem Cell and Regenerative Biology Program, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kimberly M. Christian
- Mahoney Institute for Neurosciences, Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Genome-wide CRISPR screen for HSV-1 host factors reveals PAPSS1 contributes to heparan sulfate synthesis. Commun Biol 2022; 5:694. [PMID: 35854076 PMCID: PMC9296583 DOI: 10.1038/s42003-022-03581-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 06/10/2022] [Indexed: 12/01/2022] Open
Abstract
Herpes simplex virus type 1 (HSV-1) is a ubiquitous pathogen that causes various diseases in humans, ranging from common mucocutaneous lesions to severe life-threatening encephalitis. However, our understanding of the interaction between HSV-1 and human host factors remains incomplete. Here, to identify the host factors for HSV-1 infection, we performed a human genome-wide CRISPR screen using near-haploid HAP1 cells, in which gene knockout (KO) could be efficiently achieved. Along with several already known host factors, we identified 3′-phosphoadenosine 5′-phosphosulfate synthase 1 (PAPSS1) as a host factor for HSV-1 infection. The KO of PAPSS1 in HAP1 cells reduced heparan sulfate (HepS) expression, consequently diminishing the binding of HSV-1 and several other HepS-dependent viruses (such as HSV-2, hepatitis B virus, and a human seasonal coronavirus). Hence, our findings provide further insights into the host factor requirements for HSV-1 infection and HepS biosynthesis. A genome-wide CRISPR screen for HSV-1 host factors using near-haploid HAP1 cells revealed PAPSS1 as an essential factor for heparan sulfate biosynthesis and HSV-1 infection, and identified several other host factors also involved in both processes.
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Milhim BHGA, da Rocha LC, Terzian ACB, Mazaro CCP, Augusto MT, Luchs A, Zini N, Sacchetto L, dos Santos BF, Garcia PHC, Rocha RS, Liso E, Brienze VMS, da Silva GCD, Vasilakis N, Estofolete CF, Nogueira ML. Arboviral Infections in Neurological Disorders in Hospitalized Patients in São José do Rio Preto, São Paulo, Brazil. Viruses 2022; 14:1488. [PMID: 35891468 PMCID: PMC9323204 DOI: 10.3390/v14071488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/03/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Arbovirus infections are increasingly important causes of disease, whose spectrum of neurological manifestations are not fully known. This study sought to retrospectively assess the incidence of arboviruses in cerebrospinal fluid samples of patients with neurological symptoms to inform diagnosis of central and peripheral nervous system disorders. A total of 255 cerebrospinal fluid (CSF) samples collected from January 2016 to December 2017 were tested for dengue virus (DENV 1-4), Zika virus (ZIKV), and Chikungunya virus (CHIKV) in addition to other neurotropic arboviruses of interest, using genetic and serologic assays. Of the 255 CSF samples analyzed, 3.53% (09/255) were positive for arboviruses presenting mainly as meningitis, encephalitis, and cerebrovascular events, of which ZIKV was detected in 2.74% (7/255), DENV in 0.78% (2/255), in addition to an identified ILHV infection that was described previously. All the cases were detected in adults aged 18 to 74 years old. Our findings highlight the scientific and clinical importance of neurological syndromes associated with arboviruses and demonstrate the relevance of specific laboratory methods to achieve accurate diagnoses as well as highlight the true dimension of these diseases to ultimately improve public health planning and medical case management.
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Affiliation(s)
- Bruno H. G. A. Milhim
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Leonardo C. da Rocha
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Ana C. B. Terzian
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
- Laboratório de Imunologia Celular e Molecular (LICM), Avenida Augusto de Lima, 1715, Centro, Belo Horizonte 30190-002, MG, Brazil
- Instituto René Rachou Fundação Oswaldo Cruz, Avenida Augusto de Lima, 1715, Centro, Belo Horizonte 30190-002, MG, Brazil
| | - Carolina C. P. Mazaro
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Marcos T. Augusto
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Adriana Luchs
- Enteric Disease Laboratory, Department of Virology, Adolfo Lutz Institute, Avenida Dr. Arnaldo, 355, São Paulo 01246-902, SP, Brazil;
| | - Nathalia Zini
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Livia Sacchetto
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Barbara F. dos Santos
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Pedro H. C. Garcia
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Rodrigo S. Rocha
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Elisabete Liso
- Hospital de Base, Avenida Brigadeiro Faria Lima, 5544-Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (E.L.); (V.M.S.B.)
| | - Vânia M. S. Brienze
- Hospital de Base, Avenida Brigadeiro Faria Lima, 5544-Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (E.L.); (V.M.S.B.)
| | - Gislaine C. D. da Silva
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA;
- Department of Preventive Medicine and Population Health, The University of Texas Medical Branch, Galveston, TX 77555-1150, USA
- Center for Vector-Borne and Zoonotic Diseases, The University of Texas Medical Branch, Galveston, TX 77555-0609, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0610, USA
| | - Cássia F. Estofolete
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Maurício L. Nogueira
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA;
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Guo D, Yu X, Wang D, Li Z, Zhou Y, Xu G, Yuan B, Qin Y, Chen M. SLC35B2 Acts in a Dual Role in the Host Sulfation Required for EV71 Infection. J Virol 2022; 96:e0204221. [PMID: 35420441 PMCID: PMC9093107 DOI: 10.1128/jvi.02042-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/22/2022] [Indexed: 11/20/2022] Open
Abstract
As an important neurotropic enterovirus, enterovirus 71 (EV71) is occasionally associated with severe neurological diseases and high mortality rates in infants and young children. Understanding the interaction between host factors and EV71 will play a vital role in developing antivirals and optimizing vaccines. Here, we performed a genome-wide CRISPR-Cas9 knockout screen and revealed that scavenger receptor class B member 2 (SCARB2), solute carrier family 35 member B2 (SLC35B2), and beta-1,3-glucuronyltransferase 3 (B3GAT3) are essential in facilitating EV71 replication. Subsequently, the exploration of molecular mechanisms suggested that the knockout of SLC35B2 or B3GAT3, not SCARB2, led to a remarkable decrease in the binding of EV71 to cells and internalization into cells. Furthermore, we found that the infection efficiency for EV71 was positively correlated with the level of host cell sulfation, not simply with the amount of heparan sulfate, suggesting that an unidentified sulfated protein(s) must contribute to EV71 infection. In support of this idea, we screened possible sulfated proteins among the proteinous receptors for EV71 and confirmed that SCARB2 could uniquely interact with both tyrosyl protein sulfotransferases in humans. We then performed mass spectrometric analysis of SCARB2, identifying five sites with tyrosine sulfation. The function verification test indicated that there were more than five tyrosine-sulfated sites on SCARB2. Finally, we constructed a model for EV71 entry in which both heparan sulfate and SCARB2 are regulated by SLC35B2 and act cooperatively to support viral binding, internalization, and uncoating. Taken together, this is the first time that we performed the pooled CRISPR-Cas9 genetic screening to investigate the interplay of host cells and EV71. Furthermore, we found that a novel host factor, SLC35B2, played a dual role in regulating the overall sulfation comprising heparan sulfate sulfation and protein tyrosine sulfation, which are critical for EV71 entry. IMPORTANCE As the most important nonpolio neurotropic enterovirus lacking specific treatments, EV71 can transmit to the central nervous system, leading to severe and fatal neurological complications in infants and young children. The identification of new factors that facilitate or inhibit EV71 replication is crucial to uncover the mechanisms of viral infection and pathogenesis. To date, only a few host factors involved in EV71 infection have been characterized. Herein, we conducted a genome-wide CRISPR-Cas9 functional knockout (GeCKO) screen for the first time to study EV71 in HeLa cells. The screening results are presented as a ranked list of candidates, including 518 hits in the positive selection that facilitate EV71 replication and 1,044 hits in the negative selection that may be essential for cell growth and survival or for suppressing EV71 infection. We subsequently concentrated on the top three hits in the positive selection: SCARB2, SLC35B2, and B3GAT3. The knockout of any of these three genes confers strong resistance against EV71 infection. We confirmed that EV71 infection is codependent on two receptors, heparan sulfate and SCARB2. We also identified a host entry factor, SLC35B2, indirectly facilitating EV71 infection through regulation of the host cell sulfation, and determined a novel posttranslational modification, protein tyrosine sulfation existing in SCARB2. This study revealed that EV71 infectivity exhibits a significant positive correlation with the level of cellular sulfation regulated by SLC35B2. Due to the sulfation pathway being required for many distinct viruses, including but not limited to EV71 and respiratory syncytial virus (RSV), which were tested in this study, SLC35B2 represents a target of broad-spectrum antiviral therapy.
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Affiliation(s)
- Dong Guo
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xinghai Yu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Dan Wang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhifei Li
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Zhou
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Guodong Xu
- Wuhan Canvest Biotechnology Co., Ltd., Wuhan, Hubei, China
| | - Bing Yuan
- Wuhan Canvest Biotechnology Co., Ltd., Wuhan, Hubei, China
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mingzhou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
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Vazquez C, Jurado KA. Neurotropic RNA Virus Modulation of Immune Responses within the Central Nervous System. Int J Mol Sci 2022; 23:ijms23074018. [PMID: 35409387 PMCID: PMC8999457 DOI: 10.3390/ijms23074018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 12/16/2022] Open
Abstract
The central nervous system (CNS) necessitates intricately coordinated immune responses to prevent neurological disease. However, the emergence of viruses capable of entering the CNS and infecting neurons threatens this delicate balance. Our CNS is protected from foreign invaders and excess solutes by a semipermeable barrier of endothelial cells called the blood–brain barrier. Thereby, viruses have implemented several strategies to bypass this protective layer and modulate immune responses within the CNS. In this review, we outline these immune regulatory mechanisms and provide perspectives on future questions in this rapidly expanding field.
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Gullo G, Scaglione M, Cucinella G, Riva A, Coldebella D, Cavaliere AF, Signore F, Buzzaccarini G, Spagnol G, Laganà AS, Noventa M, Zaami S. Congenital Zika Syndrome: Genetic Avenues for Diagnosis and Therapy, Possible Management and Long-Term Outcomes. J Clin Med 2022; 11:jcm11051351. [PMID: 35268441 PMCID: PMC8911172 DOI: 10.3390/jcm11051351] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Zika virus (ZIKV) was discovered in Uganda in 1947 and was originally isolated only in Africa and Asia. After a spike of microcephaly cases in Brazil, research has closely focused on different aspects of congenital ZIKV infection. In this review, we evaluated many aspects of the disease in order to build its natural history, with a focus on the long-term clinical and neuro-radiological outcomes in children. The authors have conducted a wide-ranging search spanning the 2012–2021 period from databases PubMed, PubMed Central, Web of Science, Medline, Scopus. Different sections reflect different points of congenital ZIKV infection syndrome: pathogenesis, prenatal diagnosis, clinical signs, neuroimaging and long-term developmental outcomes. It emerged that pathogenesis has not been fully clarified and that the clinical signs are not only limited to microcephaly. Given the current absence of treatments, we proposed schemes to optimize diagnostic protocols in endemic countries. It is essential to know the key aspects of this disease to guarantee early diagnosis, even in less severe cases, and an adequate management of the main chronic problems. Considering the relatively recent discovery of this congenital infectious syndrome, further studies and updated long-term follow-up are needed to further improve management strategies for this disease.
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Affiliation(s)
- Giuseppe Gullo
- Department of Obstetrics and Gynecology, Villa Sofia Cervello Hospital IVF UNIT, University of Palermo, 90146 Palermo, Italy; (G.G.); (G.C.)
| | - Marco Scaglione
- School of Medicine and Surgery, University of Palermo, 90127 Palermo, Italy;
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90133 Palermo, Italy
| | - Gaspare Cucinella
- Department of Obstetrics and Gynecology, Villa Sofia Cervello Hospital IVF UNIT, University of Palermo, 90146 Palermo, Italy; (G.G.); (G.C.)
| | - Arianna Riva
- Department of Women’s and Children’s Health, Padova Hospital, 35128 Padova, Italy;
| | - Davide Coldebella
- Department of Women’s and Children’s Health, Gynaecological Clinic, University of Padova, 35128 Padova, Italy; (D.C.); (G.B.); (G.S.); (M.N.)
| | - Anna Franca Cavaliere
- Department of Gynecology and Obstetrics, Santo Stefano Hospital, ULS Toscana Centro, 59100 Rome, Italy;
| | - Fabrizio Signore
- Department of Gynecology and Obstetrics, Sant’Eugenio Hospital, 00144 Rome, Italy;
| | - Giovanni Buzzaccarini
- Department of Women’s and Children’s Health, Gynaecological Clinic, University of Padova, 35128 Padova, Italy; (D.C.); (G.B.); (G.S.); (M.N.)
| | - Giulia Spagnol
- Department of Women’s and Children’s Health, Gynaecological Clinic, University of Padova, 35128 Padova, Italy; (D.C.); (G.B.); (G.S.); (M.N.)
| | - Antonio Simone Laganà
- Department of Obstetrics and Gynecology, “Filippo Del Ponte” Hospital, University of Insubria, 21100 Varese, Italy;
| | - Marco Noventa
- Department of Women’s and Children’s Health, Gynaecological Clinic, University of Padova, 35128 Padova, Italy; (D.C.); (G.B.); (G.S.); (M.N.)
| | - Simona Zaami
- Department of Anatomical, Histological, Forensic and Orthopedic Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
- Correspondence:
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31
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Schneider WM, Hoffmann HH. Flavivirus-host interactions: an expanding network of proviral and antiviral factors. Curr Opin Virol 2022; 52:71-77. [PMID: 34896863 PMCID: PMC8655497 DOI: 10.1016/j.coviro.2021.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 02/07/2023]
Abstract
Flaviviruses are zoonotic pathogens transmitted by the bite of infected mosquitos and ticks and represent a constant burden to human health. Here we review recent literature aimed at uncovering how flaviviruses interact with the cells that they infect. A better understanding of these interactions may ultimately lead to novel therapeutic targets. We highlight several studies that employed low-biased methods to discover new protein-protein, protein-RNA, and genetic interactions, and spotlight recent work characterizing the host protein, TMEM41B, which has been shown to be critical for infection by diverse flaviviruses and coronaviruses.
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Affiliation(s)
- William M Schneider
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
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32
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Hanrath AT, Hatton CF, Gothe F, Browne C, Vowles J, Leary P, Cockell SJ, Cowley SA, James WS, Hambleton S, Duncan CJA. Type I interferon receptor ( IFNAR2) deficiency reveals Zika virus cytopathicity in human macrophages and microglia. Front Immunol 2022; 13:1035532. [PMID: 36439115 PMCID: PMC9691778 DOI: 10.3389/fimmu.2022.1035532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/21/2022] [Indexed: 11/13/2022] Open
Abstract
Macrophages are key target cells of Zika virus (ZIKV) infection, implicated as a viral reservoir seeding sanctuary sites such as the central nervous system and testes. This rests on the apparent ability of macrophages to sustain ZIKV replication without experiencing cytopathic effects. ZIKV infection of macrophages triggers an innate immune response involving type I interferons (IFN-I), key antiviral cytokines that play a complex role in ZIKV pathogenesis in animal models. To investigate the functional role of the IFN-I response we generated human induced pluripotent stem cell (iPSC)-derived macrophages from a patient with complete deficiency of IFNAR2, the high affinity IFN-I receptor subunit. Accompanying the profound defect of IFN-I signalling in IFNAR2 deficient iPS-macrophages we observed significantly enhanced ZIKV replication and cell death, revealing the inherent cytopathicity of ZIKV towards macrophages. These observations were recapitulated by genetic and pharmacological ablation of IFN-I signalling in control iPS-macrophages and extended to a model of iPS-microglia. Thus, the capacity of macrophages to support noncytolytic ZIKV replication depends on an equilibrium set by IFN-I, suggesting that innate antiviral responses might counterintuitively promote ZIKV persistence via the maintenance of tissue viral reservoirs relevant to pathogenesis.
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Affiliation(s)
- Aidan T Hanrath
- Immunology and Inflammation Theme, Translational and Clinical Research Institute, Newcastle University, Newcastle, United Kingdom.,Department of Infection and Tropical Medicine, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Catherine F Hatton
- Immunology and Inflammation Theme, Translational and Clinical Research Institute, Newcastle University, Newcastle, United Kingdom.,Department of Infection and Tropical Medicine, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Florian Gothe
- Immunology and Inflammation Theme, Translational and Clinical Research Institute, Newcastle University, Newcastle, United Kingdom
| | - Cathy Browne
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Jane Vowles
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Peter Leary
- Bioinformatics Support Unit, Newcastle University, Newcastle, United Kingdom
| | - Simon J Cockell
- Bioinformatics Support Unit, Newcastle University, Newcastle, United Kingdom.,School of Biomedical, Nutritional and Sports Sciences, Newcastle University, Newcastle, United Kingdom
| | - Sally A Cowley
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - William S James
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Sophie Hambleton
- Immunology and Inflammation Theme, Translational and Clinical Research Institute, Newcastle University, Newcastle, United Kingdom.,Department of Paediatric Immunology and Infectious Diseases, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Christopher J A Duncan
- Immunology and Inflammation Theme, Translational and Clinical Research Institute, Newcastle University, Newcastle, United Kingdom.,Department of Infection and Tropical Medicine, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom.,Bioinformatics Support Unit, Newcastle University, Newcastle, United Kingdom
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Tripathi D, Sodani M, Gupta PK, Kulkarni S. Host directed therapies: COVID-19 and beyond. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2021; 2:100058. [PMID: 34870156 PMCID: PMC8464038 DOI: 10.1016/j.crphar.2021.100058] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/14/2021] [Accepted: 09/19/2021] [Indexed: 12/15/2022] Open
Abstract
The global spread of SARS-CoV-2 has necessitated the development of novel, safe and effective therapeutic agents against this virus to stop the pandemic, however the development of novel antivirals may take years, hence, the best alternative available, is to repurpose the existing antiviral drugs with known safety profile in humans. After more than one year into this pandemic, global efforts have yielded the fruits and with the launch of many vaccines in the market, the world is inching towards the end of this pandemic, nonetheless, future pandemics of this magnitude or even greater cannot be denied. The preparedness against viruses of unknown origin should be maintained and the broad-spectrum antivirals with activity against range of viruses should be developed to curb future viral pandemics. The majority of antivirals developed till date are pathogen specific agents, which target critical viral pathways and lack broad spectrum activity required to target wide range of viruses. The surge in drug resistance among pathogens has rendered a compelling need to shift our focus towards host directed factors in the treatment of infectious diseases. This gains special relevance in the case of viral infections, where the pathogen encodes a handful of genes and predominantly depends on host factors for their propagation and persistence. Therefore, future antiviral drug development should focus more on targeting molecules of host pathways that are often hijacked by many viruses. Such cellular proteins of host pathways offer attractive targets for the development of broad-spectrum anticipatory antivirals. In the present article, we have reviewed the host directed therapies (HDTs) effective against viral infections with a special focus on COVID-19. This article also discusses the strategies involved in identifying novel host targets and subsequent development of broad spectrum HDTs.
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Affiliation(s)
- Devavrat Tripathi
- Radiation Medicine Centre, Bhabha Atomic Research Centre, C/O Tata Memorial Hospital Annexe, Parel, Mumbai, 400012, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Megha Sodani
- Radiation Medicine Centre, Bhabha Atomic Research Centre, C/O Tata Memorial Hospital Annexe, Parel, Mumbai, 400012, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Pramod Kumar Gupta
- Radiation Medicine Centre, Bhabha Atomic Research Centre, C/O Tata Memorial Hospital Annexe, Parel, Mumbai, 400012, India
- Corresponding author.
| | - Savita Kulkarni
- Radiation Medicine Centre, Bhabha Atomic Research Centre, C/O Tata Memorial Hospital Annexe, Parel, Mumbai, 400012, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
- Corresponding author. Radiation Medicine Centre, Bhabha Atomic Research Centre, C/O Tata Memorial Hospital Annexe, Parel, Mumbai, 400012, India.
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Petit MJ, Kenaston MW, Pham OH, Nagainis AA, Fishburn AT, Shah PS. Nuclear dengue virus NS5 antagonizes expression of PAF1-dependent immune response genes. PLoS Pathog 2021; 17:e1010100. [PMID: 34797876 PMCID: PMC8641875 DOI: 10.1371/journal.ppat.1010100] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 12/03/2021] [Accepted: 11/08/2021] [Indexed: 12/24/2022] Open
Abstract
Dengue virus (DENV) disruption of the innate immune response is critical to establish infection. DENV non-structural protein 5 (NS5) plays a central role in this disruption, such as antagonism of STAT2. We recently found that DENV serotype 2 (DENV2) NS5 interacts with Polymerase associated factor 1 complex (PAF1C). The primary members of PAF1C are PAF1, LEO1, CTR9, and CDC73. This nuclear complex is an emerging player in the immune response. It promotes the expression of many genes, including genes related to the antiviral, antimicrobial and inflammatory responses, through close association with the chromatin of these genes. Our previous work demonstrated that NS5 antagonizes PAF1C recruitment to immune response genes. However, it remains unknown if NS5 antagonism of PAF1C is complementary to its antagonism of STAT2. Here, we show that knockout of PAF1 enhances DENV2 infectious virion production. By comparing gene expression profiles in PAF1 and STAT2 knockout cells, we find that PAF1 is necessary to express immune response genes that are STAT2-independent. Finally, we mapped the viral determinants for the NS5-PAF1C protein interaction. We found that NS5 nuclear localization and the C-terminal region of the methyltransferase domain are required for its interaction with PAF1C. Mutation of these regions rescued the expression of PAF1-dependent immune response genes that are antagonized by NS5. In sum, our results support a role for PAF1C in restricting DENV2 replication that NS5 antagonizes through its protein interaction with PAF1C. Dengue virus (DENV) is a pathogen that infects nearly 400 million people a year and thus represents a major challenge for public health. Productive infection by DENV relies on the effective evasion of intrinsic antiviral defenses and is often accomplished through virus-host protein interactions. Here, we investigate the recently discovered interaction between DENV non-structural protein 5 (NS5) and the transcriptional regulator Polymerase associated factor 1 complex (PAF1C). Our work demonstrates PAF1C member PAF1 acts as an antiviral factor and inhibits DENV replication. In parallel, we identified immune response genes involved in intrinsic antiviral defense that depend on PAF1 for expression. We further identified the regions of NS5 required for the protein interaction with PAF1C. Breaking the NS5-PAF1C protein interaction restores the expression of PAF1-dependent immune response genes. Together, our work establishes the antiviral role of PAF1C in DENV infection and NS5 antagonism of PAF1-dependent gene expression through a virus-host protein interaction.
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Affiliation(s)
- Marine J. Petit
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
- Department of Chemical Engineering, University of California, Davis, California, United States of America
| | - Matthew W. Kenaston
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
| | - Oanh H. Pham
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
| | - Ariana A. Nagainis
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
- Department of Chemical Engineering, University of California, Davis, California, United States of America
| | - Adam T. Fishburn
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
| | - Priya S. Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, United States of America
- Department of Chemical Engineering, University of California, Davis, California, United States of America
- * E-mail:
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35
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Synowiec A, Jedrysik M, Branicki W, Klajmon A, Lei J, Owczarek K, Suo C, Szczepanski A, Wang J, Zhang P, Labaj PP, Pyrc K. Identification of Cellular Factors Required for SARS-CoV-2 Replication. Cells 2021; 10:cells10113159. [PMID: 34831382 PMCID: PMC8622730 DOI: 10.3390/cells10113159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/27/2021] [Accepted: 11/10/2021] [Indexed: 12/25/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the recently emerged virus responsible for the COVID-19 pandemic. Clinical presentation can range from asymptomatic disease and mild respiratory tract infection to severe disease with lung injury, multiorgan failure, and death. SARS-CoV-2 is the third animal coronavirus to emerge in humans in the 21st century, and coronaviruses appear to possess a unique ability to cross borders between species and infect a wide range of organisms. This is somewhat surprising as, except for the requirement of host cell receptors, cell–pathogen interactions are usually species-specific. Insights into these host–virus interactions will provide a deeper understanding of the process of SARS-CoV-2 infection and provide a means for the design and development of antiviral agents. In this study, we describe a complex analysis of SARS-CoV-2 infection using a genome-wide CRISPR-Cas9 knock-out system in HeLa cells overexpressing entry receptor angiotensin-converting enzyme 2 (ACE2). This platform allows for the identification of factors required for viral replication. This study was designed to include a high number of replicates (48 replicates; 16 biological repeats with 3 technical replicates each) to prevent data instability, remove sources of bias, and allow multifactorial bioinformatic analyses in order to study the resulting interaction network. The results obtained provide an interesting insight into the replication mechanisms of SARS-CoV-2.
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Affiliation(s)
- Aleksandra Synowiec
- ViroGenetics—BSL3 Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; (A.S.); (M.J.); (K.O.); (A.S.)
| | - Malwina Jedrysik
- ViroGenetics—BSL3 Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; (A.S.); (M.J.); (K.O.); (A.S.)
| | - Wojciech Branicki
- Human Genome Variation Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; (W.B.); (A.K.)
| | - Adrianna Klajmon
- Human Genome Variation Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; (W.B.); (A.K.)
| | - Jing Lei
- Key Laboratory of Public Health Safety, Department of Epidemiology & Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, China; (J.L.); (C.S.); (J.W.); (P.Z.)
| | - Katarzyna Owczarek
- ViroGenetics—BSL3 Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; (A.S.); (M.J.); (K.O.); (A.S.)
| | - Chen Suo
- Key Laboratory of Public Health Safety, Department of Epidemiology & Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, China; (J.L.); (C.S.); (J.W.); (P.Z.)
- Taizhou Institute of Health Sciences, Fudan University, Taizhou 225316, China
| | - Artur Szczepanski
- ViroGenetics—BSL3 Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; (A.S.); (M.J.); (K.O.); (A.S.)
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Jingru Wang
- Key Laboratory of Public Health Safety, Department of Epidemiology & Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, China; (J.L.); (C.S.); (J.W.); (P.Z.)
| | - Pengyan Zhang
- Key Laboratory of Public Health Safety, Department of Epidemiology & Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, China; (J.L.); (C.S.); (J.W.); (P.Z.)
| | - Pawel P. Labaj
- Bioinformatics Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
- Correspondence: (P.P.L.); (K.P.)
| | - Krzysztof Pyrc
- ViroGenetics—BSL3 Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; (A.S.); (M.J.); (K.O.); (A.S.)
- Correspondence: (P.P.L.); (K.P.)
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Chulanov V, Kostyusheva A, Brezgin S, Ponomareva N, Gegechkori V, Volchkova E, Pimenov N, Kostyushev D. CRISPR Screening: Molecular Tools for Studying Virus-Host Interactions. Viruses 2021; 13:v13112258. [PMID: 34835064 PMCID: PMC8618713 DOI: 10.3390/v13112258] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas is a powerful tool for studying the role of genes in viral infections. The invention of CRISPR screening technologies has made it possible to untangle complex interactions between the host and viral agents. Moreover, whole-genome and pathway-specific CRISPR screens have facilitated identification of novel drug candidates for treating viral infections. In this review, we highlight recent developments in the fields of CRISPR/Cas with a focus on the use of CRISPR screens for studying viral infections and identifying new candidate genes to aid development of antivirals.
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Affiliation(s)
- Vladimir Chulanov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (V.C.); (A.K.); (S.B.); (N.P.); (N.P.)
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Infectious Diseases, Sechenov University, 119991 Moscow, Russia;
| | - Anastasiya Kostyusheva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (V.C.); (A.K.); (S.B.); (N.P.); (N.P.)
| | - Sergey Brezgin
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (V.C.); (A.K.); (S.B.); (N.P.); (N.P.)
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Natalia Ponomareva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (V.C.); (A.K.); (S.B.); (N.P.); (N.P.)
- Department of Pharmaceutical and Toxicological Chemistry, Sechenov University, 119991 Moscow, Russia;
| | - Vladimir Gegechkori
- Department of Pharmaceutical and Toxicological Chemistry, Sechenov University, 119991 Moscow, Russia;
| | - Elena Volchkova
- Department of Infectious Diseases, Sechenov University, 119991 Moscow, Russia;
| | - Nikolay Pimenov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (V.C.); (A.K.); (S.B.); (N.P.); (N.P.)
| | - Dmitry Kostyushev
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (V.C.); (A.K.); (S.B.); (N.P.); (N.P.)
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Infectious Diseases, Sechenov University, 119991 Moscow, Russia;
- Correspondence:
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37
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McTague A, Rossignoli G, Ferrini A, Barral S, Kurian MA. Genome Editing in iPSC-Based Neural Systems: From Disease Models to Future Therapeutic Strategies. Front Genome Ed 2021; 3:630600. [PMID: 34713254 PMCID: PMC8525405 DOI: 10.3389/fgeed.2021.630600] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/19/2021] [Indexed: 12/14/2022] Open
Abstract
Therapeutic advances for neurological disorders are challenging due to limited accessibility of the human central nervous system and incomplete understanding of disease mechanisms. Many neurological diseases lack precision treatments, leading to significant disease burden and poor outcome for affected patients. Induced pluripotent stem cell (iPSC) technology provides human neuronal cells that facilitate disease modeling and development of therapies. The use of genome editing, in particular CRISPR-Cas9 technology, has extended the potential of iPSCs, generating new models for a number of disorders, including Alzheimers and Parkinson Disease. Editing of iPSCs, in particular with CRISPR-Cas9, allows generation of isogenic pairs, which differ only in the disease-causing mutation and share the same genetic background, for assessment of phenotypic differences and downstream effects. Moreover, genome-wide CRISPR screens allow high-throughput interrogation for genetic modifiers in neuronal phenotypes, leading to discovery of novel pathways, and identification of new therapeutic targets. CRISPR-Cas9 has now evolved beyond altering gene expression. Indeed, fusion of a defective Cas9 (dCas9) nuclease with transcriptional repressors or activation domains allows down-regulation or activation of gene expression (CRISPR interference, CRISPRi; CRISPR activation, CRISPRa). These new tools will improve disease modeling and facilitate CRISPR and cell-based therapies, as seen for epilepsy and Duchenne muscular dystrophy. Genome engineering holds huge promise for the future understanding and treatment of neurological disorders, but there are numerous barriers to overcome. The synergy of iPSC-based model systems and gene editing will play a vital role in the route to precision medicine and the clinical translation of genome editing-based therapies.
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Affiliation(s)
- Amy McTague
- Developmental Neurosciences, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Department of Neurology, Great Ormond Street Hospital, London, United Kingdom
| | - Giada Rossignoli
- Developmental Neurosciences, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Arianna Ferrini
- Developmental Neurosciences, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Serena Barral
- Developmental Neurosciences, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Manju A Kurian
- Developmental Neurosciences, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Department of Neurology, Great Ormond Street Hospital, London, United Kingdom
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38
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Kirby EN, Shue B, Thomas PQ, Beard MR. CRISPR Tackles Emerging Viral Pathogens. Viruses 2021; 13:2157. [PMID: 34834963 PMCID: PMC8624524 DOI: 10.3390/v13112157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 12/17/2022] Open
Abstract
Understanding the dynamic relationship between viral pathogens and cellular host factors is critical to furthering our knowledge of viral replication, disease mechanisms and development of anti-viral therapeutics. CRISPR genome editing technology has enhanced this understanding, by allowing identification of pro-viral and anti-viral cellular host factors for a wide range of viruses, most recently the cause of the COVID-19 pandemic, SARS-CoV-2. This review will discuss how CRISPR knockout and CRISPR activation genome-wide screening methods are a robust tool to investigate the viral life cycle and how other class 2 CRISPR systems are being repurposed for diagnostics.
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Affiliation(s)
- Emily N. Kirby
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia; (E.N.K.); (B.S.)
| | - Byron Shue
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia; (E.N.K.); (B.S.)
| | - Paul Q. Thomas
- Adelaide Medical School, The University of Adelaide, Adelaide 5000, Australia;
- Robinson Research Institute, The University of Adelaide, Adelaide 5006, Australia
- Genome Editing Program, South Australian Health & Medical Research Institute, North Terrace, Adelaide 5000, Australia
| | - Michael R. Beard
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia; (E.N.K.); (B.S.)
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A CRISPR Activation Screen Identifies an Atypical Rho GTPase That Enhances Zika Viral Entry. Viruses 2021; 13:v13112113. [PMID: 34834920 PMCID: PMC8623001 DOI: 10.3390/v13112113] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/14/2022] Open
Abstract
Zika virus (ZIKV) is a re-emerging flavivirus that has caused large-scale epidemics. Infection during pregnancy can lead to neurologic developmental abnormalities in children. There is no approved vaccine or therapy for ZIKV. To uncover cellular pathways required for ZIKV that can be therapeutically targeted, we transcriptionally upregulated all known human coding genes with an engineered CRISPR-Cas9 activation complex in human fibroblasts deficient in interferon (IFN) signaling. We identified Ras homolog family member V (RhoV) and WW domain-containing transcription regulator 1 (WWTR1) as proviral factors, and found them to play important roles during early ZIKV infection in A549 cells. We then focused on RhoV, a Rho GTPase with atypical terminal sequences and membrane association, and validated its proviral effects on ZIKV infection and virion production in SNB-19 cells. We found that RhoV promotes infection of some flaviviruses and acts at the step of viral entry. Furthermore, RhoV proviral effects depend on the complete GTPase cycle. By depleting Rho GTPases and related proteins, we identified RhoB and Pak1 as additional proviral factors. Taken together, these results highlight the positive role of RhoV in ZIKV infection and confirm CRISPR activation as a relevant method to identify novel host-pathogen interactions.
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Volland A, Lohmüller M, Heilmann E, Kimpel J, Herzog S, von Laer D. Heparan sulfate proteoglycans serve as alternative receptors for low affinity LCMV variants. PLoS Pathog 2021; 17:e1009996. [PMID: 34648606 PMCID: PMC8547738 DOI: 10.1371/journal.ppat.1009996] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/26/2021] [Accepted: 09/30/2021] [Indexed: 12/16/2022] Open
Abstract
Members of the Old World Arenaviruses primarily utilize α-dystroglycan (α-DAG1) as a cellular receptor for infection. Mutations within the glycoprotein (GP) of lymphocytic choriomeningitis virus (LCMV) reduce or abrogate the binding affinity to α-DAG1 and thus influence viral persistence, kinetics, and cell tropism. The observation that α-DAG1 deficient cells are still highly susceptible to low affinity variants, suggests the use of an alternative receptor(s). In this study, we used a genome-wide CRISPR Cas9 knockout screen in DAG1 deficient 293T cells to identify host factors involved in α-DAG1-independent LCMV infection. By challenging cells with vesicular stomatitis virus (VSV), pseudotyped with the GP of LCMV WE HPI (VSV-GP), we identified the heparan sulfate (HS) biosynthesis pathway as an important host factor for low affinity LCMV infection. These results were confirmed by a genetic approach targeting EXTL3, a key factor in the HS biosynthesis pathway, as well as by enzymatic and chemical methods. Interestingly, a single point mutation within GP1 (S153F or Y155H) of WE HPI is sufficient for the switch from DAG1 to HS binding. Furthermore, we established a simple and reliable virus-binding assay, using directly labelled VSV-GP by intramolecular fusion of VSV-P and mWasabi, demonstrating the importance of HS for virus attachment but not entry in Burkitt lymphoma cells after reconstitution of HS expression. Collectively, our study highlights the essential role of HS for low affinity LCMV infection in contrast to their high affinity counterparts. Residual LCMV infection in double knockouts indicate the use of (a) still unknown entry receptor(s).
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Affiliation(s)
- André Volland
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
- * E-mail: (AV); (DVL)
| | - Michael Lohmüller
- Division of Developmental Immunology, Medical University of Innsbruck, Innsbruck, Austria
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | - Janine Kimpel
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Herzog
- Division of Developmental Immunology, Medical University of Innsbruck, Innsbruck, Austria
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
- * E-mail: (AV); (DVL)
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Genome-wide CRISPR screen identifies RACK1 as a critical host factor for flavivirus replication. J Virol 2021; 95:e0059621. [PMID: 34586867 PMCID: PMC8610583 DOI: 10.1128/jvi.00596-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cellular factors have important roles in all facets of the flavivirus replication cycle. Deciphering viral-host protein interactions is essential for understanding the flavivirus lifecycle as well as development of effective antiviral strategies. To uncover novel host factors that are co-opted by multiple flaviviruses, a CRISPR/Cas9 genome wide knockout (KO) screen was employed to identify genes required for replication of Zika virus (ZIKV). Receptor for Activated Protein C Kinase 1 (RACK1) was identified as a novel host factor required for ZIKV replication, which was confirmed via complementary experiments. Depletion of RACK1 via siRNA demonstrated that RACK1 is important for replication of a wide range of mosquito- and tick-borne flaviviruses, including West Nile Virus (WNV), Dengue Virus (DENV), Powassan Virus (POWV) and Langat Virus (LGTV) as well as the coronavirus SARS-CoV-2, but not for YFV, EBOV, VSV or HSV. Notably, flavivirus replication was only abrogated when RACK1 expression was dampened prior to infection. Utilising a non-replicative flavivirus model, we show altered morphology of viral replication factories and reduced formation of vesicle packets (VPs) in cells lacking RACK1 expression. In addition, RACK1 interacted with NS1 protein from multiple flaviviruses; a key protein for replication complex formation. Overall, these findings reveal RACK1's crucial role to the biogenesis of pan-flavivirus replication organelles. Importance Cellular factors are critical in all facets of viral lifecycles, where overlapping interactions between the virus and host can be exploited as possible avenues for the development of antiviral therapeutics. Using a genome-wide CRISPR knock-out screening approach to identify novel cellular factors important for flavivirus replication we identified RACK1 as a pro-viral host factor for both mosquito- and tick-borne flaviviruses in addition to SARS-CoV-2. Using an innovative flavivirus protein expression system, we demonstrate for the first time the impact of the loss of RACK1 on the formation of viral replication factories known as 'vesicle packets' (VPs). In addition, we show that RACK1 can interact with numerous flavivirus NS1 proteins as a potential mechanism by which VP formation can be induced by the former.
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Ferraris P, Wichit S, Cordel N, Missé D. Human host genetics and susceptibility to ZIKV infection. INFECTION GENETICS AND EVOLUTION 2021; 95:105066. [PMID: 34487865 DOI: 10.1016/j.meegid.2021.105066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 08/29/2021] [Accepted: 09/01/2021] [Indexed: 12/26/2022]
Abstract
Managing emerging infectious diseases is a current challenge in the fields of microbiology and epidemiology. Indeed, among other environmental and human-related factors, climate change and global warming favor the emergence of new pathogens. The recent Zika virus (ZIKV) epidemic, of which the large and rapid spread surprised the scientific community, is a reminder of the importance to study viruses currently responsible for sporadic infections. Increasing our knowledge of key factors involved in emerging infections is essential to implement specific monitoring that can be oriented according to the pathogen, targeted population, or at-risk environment. Recent technological developments, such as high-throughput sequencing, genome-wide association studies and CRISPR screenings have allowed the identification of human single nucleotide polymorphisms (SNPs) involved in infectious disease outcome. This review focuses on the human genetic host factors that have been identified and shown to be associated with the pathogenesis of ZIKV infection and candidate SNP targets.
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Affiliation(s)
- Pauline Ferraris
- MIVEGEC, Univ. Montpellier, IRD, CNRS, 34394 Montpellier, France.
| | - Sineewanlaya Wichit
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Nadège Cordel
- Guadeloupe University Hospital, Department of Dermatology and Clinical Immunology, Pointe-à-Pitre, Guadeloupe and Normandie University, UNIROUEN, IRIB, Inserm, U1234, Rouen, France
| | - Dorothée Missé
- MIVEGEC, Univ. Montpellier, IRD, CNRS, 34394 Montpellier, France
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Abstract
The CRISPR/Cas9 genome editing system has been one of the greatest scientific discoveries in the last decade. The highly efficient and precise editing ability of this technology is of great therapeutic value and benefits the basic sciences as an advantageous research tool. In recent years, forward genetic screens using CRISPR technology have been widely adopted, with genome-wide or pathway-focused screens leading to important and novel discoveries. CRISPR screens have been used primarily in cancer biology, virology, and basic cell biology, but they have rarely been applied to diabetes research. A potential reason for this is that diabetes-related research can be more complicated, often involving cross talk between multiple organs or cell types. Nevertheless, many questions can still be reduced to the study of a single cell type if assays are carefully designed. Here we review the application of CRISPR screen technology and provide perspective on how it can be used in diabetes research.
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Affiliation(s)
- Peng Yi
- Section for Islet Cell and Regenerative Biology, and CRISPR Screen Core Laboratory, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Noelle Morrow
- Section for Islet Cell and Regenerative Biology, and CRISPR Screen Core Laboratory, Joslin Diabetes Center, Harvard Medical School, Boston, MA
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Sapp V, Aguirre A, Mainkar G, Ding J, Adler E, Liao R, Sharma S, Jain M. Genome-wide CRISPR/Cas9 screening in human iPS derived cardiomyocytes uncovers novel mediators of doxorubicin cardiotoxicity. Sci Rep 2021; 11:13866. [PMID: 34230586 PMCID: PMC8260754 DOI: 10.1038/s41598-021-92988-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 05/25/2021] [Indexed: 12/26/2022] Open
Abstract
Human induced pluripotent stem (iPS) cell technologies coupled with genetic engineering now facilitate the study of the molecular underpinnings of disease in relevant human cell types. Application of CRISPR/Cas9-based approaches for genome-scale functional screening in iPS-derived cells, however, has been limited by technical constraints, including inefficient transduction in pooled format, loss of library representation, and poor cellular differentiation. Herein, we present optimized approaches for whole-genome CRISPR/Cas9 based screening in human iPS derived cardiomyocytes with near genome-wide representation at both the iPS and differentiated cell stages. As proof-of-concept, we perform a screen to investigate mechanisms underlying doxorubicin mediated cell death in iPS derived cardiomyocytes. We identified two poorly characterized, human-specific transporters (SLCO1A2, SLCO1B3) whose loss of function protects against doxorubicin-cardiotoxicity, but does not affect cell death in cancer cells. This study provides a technical framework for genome-wide functional screening in iPS derived cells and identifies new targets to mitigate doxorubicin-cardiotoxicity in humans.
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Affiliation(s)
- Valerie Sapp
- Department of Medicine, University of California, San Diego, San Diego, CA, USA
- Department of Pharmacology, University of California, San Diego, San Diego, CA, USA
| | - Aitor Aguirre
- Department of Medicine, University of California, San Diego, San Diego, CA, USA
- Division of Developmental and Stem Cell Biology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
| | - Gayatri Mainkar
- Department of Medicine, University of California, San Diego, San Diego, CA, USA
- Department of Pharmacology, University of California, San Diego, San Diego, CA, USA
| | - Jeffrey Ding
- Department of Medicine, University of California, San Diego, San Diego, CA, USA
- Department of Pharmacology, University of California, San Diego, San Diego, CA, USA
| | - Eric Adler
- Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Ronglih Liao
- Department of Medicine, Stanford University, Palo Alto, USA
| | - Sonia Sharma
- La Jolla Institute for Immunology, San Diego, CA, USA
| | - Mohit Jain
- Department of Medicine, University of California, San Diego, San Diego, CA, USA.
- Department of Pharmacology, University of California, San Diego, San Diego, CA, USA.
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Harschnitz O, Studer L. Human stem cell models to study host-virus interactions in the central nervous system. Nat Rev Immunol 2021; 21:441-453. [PMID: 33398129 PMCID: PMC9653304 DOI: 10.1038/s41577-020-00474-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2020] [Indexed: 01/30/2023]
Abstract
Advancements in human pluripotent stem cell technology offer a unique opportunity for the neuroimmunology field to study host-virus interactions directly in disease-relevant cells of the human central nervous system (CNS). Viral encephalitis is most commonly caused by herpesviruses, arboviruses and enteroviruses targeting distinct CNS cell types and often leading to severe neurological damage with poor clinical outcomes. Furthermore, different neurotropic viruses will affect the CNS at distinct developmental stages, from early prenatal brain development to the aged brain. With the unique flexibility and scalability of human pluripotent stem cell technology, it is now possible to examine the molecular mechanisms underlying acute infection and latency, determine which CNS subpopulations are specifically infected, study temporal aspects of viral susceptibility, perform high-throughput chemical or genetic screens for viral restriction factors and explore complex cell-non-autonomous disease mechanisms. Therefore, human pluripotent stem cell technology has the potential to address key unanswered questions about antiviral immunity in the CNS, including emerging questions on the potential CNS tropism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Oliver Harschnitz
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York (NY), USA,The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York (NY), USA,
| | - Lorenz Studer
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York (NY), USA,The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York (NY), USA
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46
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Mathez G, Cagno V. Viruses Like Sugars: How to Assess Glycan Involvement in Viral Attachment. Microorganisms 2021; 9:1238. [PMID: 34200288 PMCID: PMC8230229 DOI: 10.3390/microorganisms9061238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
The first step of viral infection requires interaction with the host cell. Before finding the specific receptor that triggers entry, the majority of viruses interact with the glycocalyx. Identifying the carbohydrates that are specifically recognized by different viruses is important both for assessing the cellular tropism and for identifying new antiviral targets. Advances in the tools available for studying glycan-protein interactions have made it possible to identify them more rapidly; however, it is important to recognize the limitations of these methods in order to draw relevant conclusions. Here, we review different techniques: genetic screening, glycan arrays, enzymatic and pharmacological approaches, and surface plasmon resonance. We then detail the glycan interactions of enterovirus D68 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlighting the aspects that need further clarification.
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Affiliation(s)
| | - Valeria Cagno
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland;
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Jones CE, Tan WS, Grey F, Hughes DJ. Discovering antiviral restriction factors and pathways using genetic screens. J Gen Virol 2021; 102. [PMID: 34020727 PMCID: PMC8295917 DOI: 10.1099/jgv.0.001603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Viral infections activate the powerful interferon (IFN) response that induces the expression of several hundred IFN stimulated genes (ISGs). The principal role of this extensive response is to create an unfavourable environment for virus replication and to limit spread; however, untangling the biological consequences of this large response is complicated. In addition to a seemingly high degree of redundancy, several ISGs are usually required in combination to limit infection as individual ISGs often have low to moderate antiviral activity. Furthermore, what ISG or combination of ISGs are antiviral for a given virus is usually not known. For these reasons, and since the function(s) of many ISGs remains unexplored, genome-wide approaches are well placed to investigate what aspects of this response result in an appropriate, virus-specific phenotype. This review discusses the advances screening approaches have provided for the study of host defence mechanisms, including clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9), ISG expression libraries and RNA interference (RNAi) technologies.
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Affiliation(s)
- Chloe E Jones
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Wenfang S Tan
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Finn Grey
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - David J Hughes
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
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Liu Y, Chang J, Yang C, Zhang T, Chen X, Shi R, Liang Y, Xia Q, Ma S. Genome-wide CRISPR-Cas9 screening in Bombyx mori reveals the toxicological mechanisms of environmental pollutants, fluoride and cadmium. JOURNAL OF HAZARDOUS MATERIALS 2021; 410:124666. [PMID: 33279320 DOI: 10.1016/j.jhazmat.2020.124666] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/27/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
Fluoride and cadmium, two typical environmental pollutants, have been extensively existed in the ecosystem and severely injured various organisms including humans. To explore the toxicological properties and the toxicological mechanism of fluoride and cadmium in silkworm, we perform a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) -based functional genomic screen, which can directly measure the genetic requirement of genes in response to the pollutants. Our screen identifies 751 NaF-resistance genes, 753 NaF-sensitive genes, 757 CdCl2-resistance genes, and 725 CdCl2-sensitive genes. The top-ranked resistant genes are experimentally verified and the results show that their loss conferred resistance to fluoride or cadmium. Functional analysis of the resistant- and sensitive-genes demonstrates enrichment of multiple signaling pathways, among which the MAPK signaling pathway and DNA damage and repair are both required for fluoride- or cadmium-induced cell death, whereas the Toll and Imd signaling pathway and Autophagy are fluoride- or cadmium-specific. Moreover, we confirm that these pathways are truly involved in the toxicological mechanism in both cultured cells and individual tissues. Our results supply potential targets for rescuing the biohazards of fluoride and cadmium in silkworm, and reveal the feasible toxicological mechanism, which highlights the role of functional genomic screens in elucidating the toxicity mechanisms of environmental pollutants.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China
| | - Jiasong Chang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China
| | - Chengfei Yang
- Department of Urology, The Second Affiliated Hospital, Army Medical University, Chongqing 400037, China
| | - Tong Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China
| | - Xiaoxu Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China
| | - Run Shi
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China
| | - Yan Liang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China.
| | - Sanyuan Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing 400716, China.
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Analysis of Zika virus capsid-Aedes aegypti mosquito interactome reveals pro-viral host factors critical for establishing infection. Nat Commun 2021; 12:2766. [PMID: 33986255 PMCID: PMC8119459 DOI: 10.1038/s41467-021-22966-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 04/06/2021] [Indexed: 02/06/2023] Open
Abstract
The escalating global prevalence of arboviral diseases emphasizes the need to improve our understanding of their biology. Research in this area has been hindered by the lack of molecular tools for studying virus-mosquito interactions. Here, we develop an Aedes aegypti cell line which stably expresses Zika virus (ZIKV) capsid proteins in order to study virus-vector protein-protein interactions through quantitative label-free proteomics. We identify 157 interactors and show that eight have potentially pro-viral activity during ZIKV infection in mosquito cells. Notably, silencing of transitional endoplasmic reticulum protein TER94 prevents ZIKV capsid degradation and significantly reduces viral replication. Similar results are observed if the TER94 ortholog (VCP) functioning is blocked with inhibitors in human cells. In addition, we show that an E3 ubiquitin-protein ligase, UBR5, mediates the interaction between TER94 and ZIKV capsid. Our study demonstrates a pro-viral function for TER94/VCP during ZIKV infection that is conserved between human and mosquito cells.
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50
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Pellegrino E, Gutierrez MG. Human stem cell-based models for studying host-pathogen interactions. Cell Microbiol 2021; 23:e13335. [PMID: 33792137 DOI: 10.1111/cmi.13335] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023]
Abstract
The use of human cell lines and primary cells as in vitro models represents a valuable approach to study cellular responses to infection. However, with the advent of new molecular technologies and tools available, there is a growing need to develop more physiologically relevant systems to overcome cell line model limitations and better mimic human disease. Since the discovery of human stem cells, its use has revolutionised the development of in vitro models. This is because after differentiation, these cells have the potential to reflect in vivo cell phenotypes and allow for probing questions in numerous fields of the biological sciences. Moreover, the possibility to combine the advantages of stem cell-derived cell types with genome editing technologies and engineered 3D microenvironments, provides enormous potential for producing in vitro systems to investigate cellular responses to infection that are both relevant and predictive. Here, we discuss recent advances in the use of human stem cells to model host-pathogen interactions, highlighting emerging technologies in the field of stem cell biology that can be exploited to investigate the fundamental biology of infection. TAKE AWAYS: hPSC overcome current limitations to study host-pathogen interactions in vitro. Genome editing can be used in hPSC to study cellular responses to infection. hPSC, 3D models and genome editing can recreate physiological in vitro systems.
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Affiliation(s)
- Enrica Pellegrino
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Maximiliano G Gutierrez
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
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