51
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Navarro-Guerrero E, Tay C, Whalley JP, Cowley SA, Davies B, Knight JC, Ebner D. Genome-wide CRISPR/Cas9-knockout in human induced Pluripotent Stem Cell (iPSC)-derived macrophages. Sci Rep 2021; 11:4245. [PMID: 33608581 PMCID: PMC7895961 DOI: 10.1038/s41598-021-82137-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 01/14/2021] [Indexed: 12/26/2022] Open
Abstract
Genome engineering using CRISPR/Cas9 technology enables simple, efficient and precise genomic modifications in human cells. Conventional immortalized cell lines can be easily edited or screened using genome-wide libraries with lentiviral transduction. However, cell types derived from the differentiation of induced Pluripotent Stem Cells (iPSC), which often represent more relevant, patient-derived models for human pathology, are much more difficult to engineer as CRISPR/Cas9 delivery to these differentiated cells can be inefficient and toxic. Here, we present an efficient, lentiviral transduction protocol for delivery of CRISPR/Cas9 to macrophages derived from human iPSC with efficiencies close to 100%. We demonstrate CRISPR/Cas9 knockouts for three nonessential proof-of-concept genes-HPRT1, PPIB and CDK4. We then scale the protocol and validate for a genome-wide pooled CRISPR/Cas9 loss-of-function screen. This methodology enables, for the first time, systematic exploration of macrophage involvement in immune responses, chronic inflammation, neurodegenerative diseases and cancer progression, using efficient genome editing techniques.
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Affiliation(s)
- Elena Navarro-Guerrero
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Chwen Tay
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Justin P Whalley
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sally A Cowley
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ben Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Daniel Ebner
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK.
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52
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Advanced single-cell pooled CRISPR screening identifies C19orf53 required for cell proliferation based on mTORC1 regulators. Cell Biol Toxicol 2021; 38:43-68. [PMID: 33586084 DOI: 10.1007/s10565-021-09586-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 02/02/2021] [Indexed: 02/07/2023]
Abstract
Multiplexed single-cell CRISPR screening has accelerated the systematic dissection of biological discoveries; however, the efficiency of CRISPR-based gene knockout has inherent limitations. Here, we present DoNick-seq, an advanced method for facilitating gene knockout and reducing off-target activity. We re-engineered two popular plasmid constructs suitable for use in pooled CRISPR screening of the single-cell transcriptome. We then used DoNick-seq to probe mTORC1 regulators and obtain genomic perturbation and transcriptome profiles from the same cell. Thus, DoNick-seq enabled us to simultaneously evaluate multiple gene interactions and the effect of amino acid depletion. By analyzing more than 20,000 cells from two cell lines, DoNick-seq efficiently identified gene targets, cell numbers, and cellular profiles. Our data also revealed the characteristics of mTORC1 negative and positive regulators, thereby shedding new insights into the mechanisms regulating cell growth and inhibition. We demonstrate that mTORC1 hyperactivation exhausts cellular free amino acids via increased proliferation ability. Furthermore, DoNick-seq identified the gene C19orf53, which mediates excessive cell proliferation, resulting in metabolic imbalance, and greatly enhances oxidative stress in response to toxins. Thus, our findings suggest that DoNick-seq facilitates high-throughput functional dissection of complex cellular responses at the single-cell level and increases the accuracy of CRISPR single-cell transcriptomics.
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53
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Rother M, Naumann M. Signal peptidase complex subunit 1 is an essential Zika virus host factor in placental trophoblasts. Virus Res 2021; 296:198338. [PMID: 33577859 DOI: 10.1016/j.virusres.2021.198338] [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: 07/17/2020] [Revised: 01/12/2021] [Accepted: 02/02/2021] [Indexed: 10/22/2022]
Abstract
Zika is a major teratogenic virus that can be transmitted from pregnant women to the fetus via the transplacental route. At present, no specific vaccines or treatments are available. Large-scale functional genomics approaches for the analysis of host cell function in infection greatly improve the understanding of molecular infection processes and advance the discovery of antiviral targets. We conducted a pooled CRISPR/Cas9 screen to explore trophoblast function upon Zika infection. The identified Zika virus host factors enrich in the ER membrane complex and the signal peptide processing pathway. Finally, we demonstrate that signal peptidase complex subunit 1 (SPCS1) is crucial for virus replication in trophoblasts.
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Affiliation(s)
- Marion Rother
- Max Planck Institute for Infection Biology, Department of Molecular Biology, 10117, Berlin, Germany; Institute of Experimental Internal Medicine, Otto Von Guericke University Magdeburg, 39120, Magdeburg, Germany.
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Otto Von Guericke University Magdeburg, 39120, Magdeburg, Germany
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54
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Rother M, Dimmler C, Weege F, Mollenkopf HJ, Meyer TF, Naumann M. Discovery of Zika virus host dependency factors in trophoblasts using CRISPR/Cas9 screening. J Virol Methods 2021; 290:114085. [PMID: 33545196 DOI: 10.1016/j.jviromet.2021.114085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/10/2021] [Accepted: 01/23/2021] [Indexed: 10/22/2022]
Abstract
Emerging mosquito-borne RNA viruses cause massive health complications worldwide. The Zika virus (ZIKV), in particular, has spread dramatically since 2007 and has provoked epidemics in the Americas and the South Pacific. The lack of antiviral therapy and vaccination has focused research on the investigation of ZIKV-host interactions, in order to understand underlying molecular infection mechanisms. We have established an approach for the analysis of ZIKV host dependency factors in a human trophoblast cell line and applied genome-wide CRISPR/Cas9 knockout mutagenesis. The presented method is especially of value for the identification of factors that are essential for placental infection with the potential to serve as targets for antiviral treatment.
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Affiliation(s)
- Marion Rother
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, 10117, Germany; Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany.
| | - Christiane Dimmler
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, 10117, Germany
| | - Friderike Weege
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, 10117, Germany
| | | | - Thomas F Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, 10117, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany
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55
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Daniloski Z, Jordan TX, Wessels HH, Hoagland DA, Kasela S, Legut M, Maniatis S, Mimitou EP, Lu L, Geller E, Danziger O, Rosenberg BR, Phatnani H, Smibert P, Lappalainen T, tenOever BR, Sanjana NE. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells. Cell 2021; 184:92-105.e16. [PMID: 33147445 PMCID: PMC7584921 DOI: 10.1016/j.cell.2020.10.030] [Citation(s) in RCA: 370] [Impact Index Per Article: 123.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/25/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022]
Abstract
To better understand host-virus genetic dependencies and find potential therapeutic targets for COVID-19, we performed a genome-scale CRISPR loss-of-function screen to identify host factors required for SARS-CoV-2 viral infection of human alveolar epithelial cells. Top-ranked genes cluster into distinct pathways, including the vacuolar ATPase proton pump, Retromer, and Commander complexes. We validate these gene targets using several orthogonal methods such as CRISPR knockout, RNA interference knockdown, and small-molecule inhibitors. Using single-cell RNA-sequencing, we identify shared transcriptional changes in cholesterol biosynthesis upon loss of top-ranked genes. In addition, given the key role of the ACE2 receptor in the early stages of viral entry, we show that loss of RAB7A reduces viral entry by sequestering the ACE2 receptor inside cells. Overall, this work provides a genome-scale, quantitative resource of the impact of the loss of each host gene on fitness/response to viral infection.
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Affiliation(s)
- Zharko Daniloski
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Tristan X Jordan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hans-Hermann Wessels
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Daisy A Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Silva Kasela
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA
| | - Mateusz Legut
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | | | - Eleni P Mimitou
- Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Lu Lu
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Evan Geller
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Oded Danziger
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hemali Phatnani
- New York Genome Center, New York, NY, USA; Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter Smibert
- Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Neville E Sanjana
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA.
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56
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Karimi-Boroujeni M, Zahedi-Amiri A, Coombs KM. Embryonic Origins of Virus-Induced Hearing Loss: Overview of Molecular Etiology. Viruses 2021; 13:71. [PMID: 33419104 PMCID: PMC7825458 DOI: 10.3390/v13010071] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 12/19/2022] Open
Abstract
Hearing loss, one of the most prevalent chronic health conditions, affects around half a billion people worldwide, including 34 million children. The World Health Organization estimates that the prevalence of disabling hearing loss will increase to over 900 million people by 2050. Many cases of congenital hearing loss are triggered by viral infections during different stages of pregnancy. However, the molecular mechanisms by which viruses induce hearing loss are not sufficiently explored, especially cases that are of embryonic origins. The present review first describes the cellular and molecular characteristics of the auditory system development at early stages of embryogenesis. These developmental hallmarks, which initiate upon axial specification of the otic placode as the primary root of the inner ear morphogenesis, involve the stage-specific regulation of several molecules and pathways, such as retinoic acid signaling, Sonic hedgehog, and Wnt. Different RNA and DNA viruses contributing to congenital and acquired hearing loss are then discussed in terms of their potential effects on the expression of molecules that control the formation of the auditory and vestibular compartments following otic vesicle differentiation. Among these viruses, cytomegalovirus and herpes simplex virus appear to have the most effect upon initial molecular determinants of inner ear development. Moreover, of the molecules governing the inner ear development at initial stages, SOX2, FGFR3, and CDKN1B are more affected by viruses causing either congenital or acquired hearing loss. Abnormalities in the function or expression of these molecules influence processes like cochlear development and production of inner ear hair and supporting cells. Nevertheless, because most of such virus-host interactions were studied in unrelated tissues, further validations are needed to confirm whether these viruses can mediate the same effects in physiologically relevant models simulating otic vesicle specification and growth.
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Affiliation(s)
- Maryam Karimi-Boroujeni
- School of Rehabilitation Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON K1H 8M5, Canada;
| | - Ali Zahedi-Amiri
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB R3E 3P4, Canada
| | - Kevin M. Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
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57
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Grand Moursel L, Visser M, Servant G, Durmus S, Zuurmond AM. CRISPRing future medicines. Expert Opin Drug Discov 2021; 16:463-473. [PMID: 33322954 DOI: 10.1080/17460441.2021.1850687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Introduction: The ability to engineer mammalian genomes in a quick and cost-effective way has led to rapid adaptation of CRISPR technology in biomedical research. CRISPR-based engineering has the potential to accelerate drug discovery, to support the reduction of high attrition rate in drug development and to enhance development of cell and gene-based therapies.Areas covered: How CRISPR technology is transforming drug discovery is discussed in this review. From target identification to target validation in both in vitro and in vivo models, CRISPR technology is positively impacting the early stages of drug development by providing a straightforward way to genome engineering. This property also attracted attention for CRISPR application in the cell and gene therapy area.Expert opinion: CRISPR technology is rapidly becoming the preferred tool for genome engineering and nowadays it is hard to imagine the drug discovery pipeline without this technology. With the years to come, CRISPR technology will undoubtedly be further refined and will flourish into a mature technology that will play a key role in supporting genome engineering requirements in the drug discovery pipeline as well as in cell and gene therapy development.
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Affiliation(s)
| | - Mijke Visser
- Charles River Laboratories, Leiden, The Netherlands
| | | | - Selvi Durmus
- Charles River Laboratories, Leiden, The Netherlands
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58
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Carro SD, Cherry S. Beyond the Surface: Endocytosis of Mosquito-Borne Flaviviruses. Viruses 2020; 13:E13. [PMID: 33374822 PMCID: PMC7824540 DOI: 10.3390/v13010013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 02/06/2023] Open
Abstract
Flaviviruses are a group of positive-sense RNA viruses that are primarily transmitted through arthropod vectors and are capable of causing a broad spectrum of diseases. Many of the flaviviruses that are pathogenic in humans are transmitted specifically through mosquito vectors. Over the past century, many mosquito-borne flavivirus infections have emerged and re-emerged, and are of global importance with hundreds of millions of infections occurring yearly. There is a need for novel, effective, and accessible vaccines and antivirals capable of inhibiting flavivirus infection and ameliorating disease. The development of therapeutics targeting viral entry has long been a goal of antiviral research, but most efforts are hindered by the lack of broad-spectrum potency or toxicities associated with on-target effects, since many host proteins necessary for viral entry are also essential for host cell biology. Mosquito-borne flaviviruses generally enter cells by clathrin-mediated endocytosis (CME), and recent studies suggest that a subset of these viruses can be internalized through a specialized form of CME that has additional dependencies distinct from canonical CME pathways, and antivirals targeting this pathway have been discovered. In this review, we discuss the role and contribution of endocytosis to mosquito-borne flavivirus entry as well as consider past and future efforts to target endocytosis for therapeutic interventions.
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Affiliation(s)
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
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59
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Genome-Wide CRISPR-Cas9 Screen Reveals the Importance of the Heparan Sulfate Pathway and the Conserved Oligomeric Golgi Complex for Synthetic Double-Stranded RNA Uptake and Sindbis Virus Infection. mSphere 2020; 5:5/6/e00914-20. [PMID: 33177215 PMCID: PMC7657590 DOI: 10.1128/msphere.00914-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
When facing a viral infection, the organism has to put in place a number of defense mechanisms in order to clear the pathogen from the cell. At the early phase of this preparation for fighting against the invader, the innate immune response is triggered by the sensing of danger signals. Among those molecular cues, double-stranded RNA (dsRNA) is a very potent inducer of different reactions at the cellular level that can ultimately lead to cell death. Using a genome-wide screening approach, we set to identify genes involved in dsRNA entry, sensing, and apoptosis induction in human cells. This allowed us to determine that the heparan sulfate pathway and the conserved oligomeric Golgi complex are key determinants allowing entry of both dsRNA and viral nucleic acid leading to cell death. Double-stranded RNA (dsRNA) is the hallmark of many viral infections. dsRNA is produced either by RNA viruses during replication or by DNA viruses upon convergent transcription. Synthetic dsRNA is also able to mimic viral-induced activation of innate immune response and cell death. In this study, we employed a genome-wide CRISPR-Cas9 loss-of-function screen based on cell survival in order to identify genes implicated in the host response to dsRNA. By challenging HCT116 human cells with either synthetic dsRNA or Sindbis virus (SINV), we identified the heparan sulfate (HS) pathway as a crucial factor for dsRNA entry, and we validated SINV dependency on HS. Interestingly, we uncovered a novel role for COG4, a component of the conserved oligomeric Golgi (COG) complex, as a factor involved in cell survival to both dsRNA and SINV in human cells. We showed that COG4 knockout led to a decrease of extracellular HS that specifically affected dsRNA transfection efficiency and reduced viral production, which explains the increased cell survival of these mutants. IMPORTANCE When facing a viral infection, the organism has to put in place a number of defense mechanisms in order to clear the pathogen from the cell. At the early phase of this preparation for fighting against the invader, the innate immune response is triggered by the sensing of danger signals. Among those molecular cues, double-stranded RNA (dsRNA) is a very potent inducer of different reactions at the cellular level that can ultimately lead to cell death. Using a genome-wide screening approach, we set to identify genes involved in dsRNA entry, sensing, and apoptosis induction in human cells. This allowed us to determine that the heparan sulfate pathway and the conserved oligomeric Golgi complex are key determinants allowing entry of both dsRNA and viral nucleic acid leading to cell death.
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60
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Genome-wide CRISPR screen identifies LGALS2 as an oxidative stress-responsive gene with an inhibitory function on colon tumor growth. Oncogene 2020; 40:177-188. [PMID: 33110234 PMCID: PMC7790754 DOI: 10.1038/s41388-020-01523-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022]
Abstract
Colorectal cancer is the third leading cause of cancer-related deaths in the United States and the third most common cancer in men and women. Around 20% colon cancer cases are closely linked with colitis. Both environmental and genetic factors are thought to contribute to colon inflammation and tumor development. However, the genetic factors regulating colitis and colon tumorigenesis remain elusive. Since reactive oxygen species (ROS) is vitally involved in tissue inflammation and tumorigenesis, here we employed a genome-wide CRISPR knockout screening approach to systemically identify the genetic factors involved in the regulation of oxidative stress. Next generation sequencing (NGS) showed that over 600 gRNAs including the ones targeting LGALS2 were highly enriched in cells survived after sublethal H2O2 challenge. LGALS2 encodes the glycan-binding protein Galectin 2 (Gal2), which is predominantly expressed in the gastrointestinal tract and downregulated in human colon tumors. To examine the role of Gal2 in colitis, we employed the dextran sodium sulfate (DSS)-induced acute colitis model in mice with (WT) or without Lgals2 (Gal2-KO) and showed that Gal2 deficiency ameliorated DSS-induced colitis. We further demonstrated that Gal2-KO mice developed significantly larger tumors than WT mice using Azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colorectal cancer model. We found that STAT3 phosphorylation was significantly increased in Gal2-deficient tumors as compared to those in WT mice. Gal2 overexpression decreased the proliferation of human colon tumor epithelial cells and blunted H2O2-induced STAT3 phosphorylation. Overall, our results demonstrate that Gal2 plays a suppressive role in colon tumor growth and highlights the therapeutic potential of Gal2 in colon cancer.
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61
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Krey K, Babnis AW, Pichlmair A. System-Based Approaches to Delineate the Antiviral Innate Immune Landscape. Viruses 2020; 12:E1196. [PMID: 33096788 PMCID: PMC7589202 DOI: 10.3390/v12101196] [Citation(s) in RCA: 5] [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: 09/25/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022] Open
Abstract
Viruses pose substantial challenges for society, economy, healthcare systems, and research. Their distinctive pathologies are based on specific interactions with cellular factors. In order to develop new antiviral treatments, it is of central importance to understand how viruses interact with their host and how infected cells react to the virus on a molecular level. Invading viruses are commonly sensed by components of the innate immune system, which is composed of a highly effective yet complex network of proteins that, in most cases, mediate efficient virus inhibition. Central to this process is the activity of interferons and other cytokines that coordinate the antiviral response. So far, numerous methods have been used to identify how viruses interact with cellular processes and revealed that the innate immune response is highly complex and involves interferon-stimulated genes and their binding partners as functional factors. Novel approaches and careful experimental design, combined with large-scale, high-throughput methods and cutting-edge analysis pipelines, have to be utilized to delineate the antiviral innate immune landscape at a global level. In this review, we describe different currently used screening approaches, how they contributed to our knowledge on virus-host interactions, and essential considerations that have to be taken into account when planning such experiments.
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Affiliation(s)
- Karsten Krey
- School of Medicine, Institute of Virology, Technical University of Munich, 81675 Munich, Germany; (K.K.); (A.W.B.)
| | - Aleksandra W. Babnis
- School of Medicine, Institute of Virology, Technical University of Munich, 81675 Munich, Germany; (K.K.); (A.W.B.)
| | - Andreas Pichlmair
- School of Medicine, Institute of Virology, Technical University of Munich, 81675 Munich, Germany; (K.K.); (A.W.B.)
- German Center for Infection Research (DZIF), Munich Partner Site, 80538 Munich, Germany
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62
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Interrogating genome function using CRISPR tools: a narrative review. JOURNAL OF BIO-X RESEARCH 2020. [DOI: 10.1097/jbr.0000000000000066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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63
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Mast FD, Navare AT, van der Sloot AM, Coulombe-Huntington J, Rout MP, Baliga NS, Kaushansky A, Chait BT, Aderem A, Rice CM, Sali A, Tyers M, Aitchison JD. Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality. J Cell Biol 2020; 219:152015. [PMID: 32785687 PMCID: PMC7659715 DOI: 10.1083/jcb.202006159] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
With the rapid global spread of SARS-CoV-2, we have become acutely aware of the inadequacies of our ability to respond to viral epidemics. Although disrupting the viral life cycle is critical for limiting viral spread and disease, it has proven challenging to develop targeted and selective therapeutics. Synthetic lethality offers a promising but largely unexploited strategy against infectious viral disease; as viruses infect cells, they abnormally alter the cell state, unwittingly exposing new vulnerabilities in the infected cell. Therefore, we propose that effective therapies can be developed to selectively target the virally reconfigured host cell networks that accompany altered cellular states to cripple the host cell that has been converted into a virus factory, thus disrupting the viral life cycle.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Arti T Navare
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Almer M van der Sloot
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Canada
| | | | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY
| | | | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Alan Aderem
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Canada
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA.,Department of Biochemistry, University of Washington, Seattle, WA
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64
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Studying Human Neurodevelopment and Diseases Using 3D Brain Organoids. J Neurosci 2020; 40:1186-1193. [PMID: 32024767 DOI: 10.1523/jneurosci.0519-19.2019] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/12/2019] [Accepted: 09/16/2019] [Indexed: 02/01/2023] Open
Abstract
In vitro differentiation of pluripotent stem cells provides a systematic platform to study development and disease. Recent advances in brain organoid technology have created new opportunities to investigate the formation and function of the human brain, under physiological and pathological conditions. Brain organoids can be generated to model the cellular and structural development of the human brain, and allow the investigation of the intricate interactions between resident neural and glial cell types. Combined with new advances in gene editing, imaging, and genomic analysis, brain organoid technology can be applied to address questions pertinent to human brain development, disease, and evolution. However, the current iterations of brain organoids also have limitations in faithfully recapitulating the in vivo processes. In this perspective, we evaluate the recent progress in brain organoid technology, and discuss the experimental considerations for its utilization.Dual Perspectives Companion Paper: Integrating CRISPR Engineering and hiPSC-Derived 2D Disease Modeling Systems, by Kristina Rehbach, Michael B. Fernando, and Kristen J. Brennand.
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65
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A Genome-Wide CRISPR-Cas9 Screen Reveals the Requirement of Host Cell Sulfation for Schmallenberg Virus Infection. J Virol 2020; 94:JVI.00752-20. [PMID: 32522852 DOI: 10.1128/jvi.00752-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
Schmallenberg virus (SBV) is an insect-transmitted orthobunyavirus that can cause abortions and congenital malformations in the offspring of ruminants. Even though the two viral surface glycoproteins Gn and Gc are involved in host cell entry, the specific cellular receptors of SBV are currently unknown. Using genome-wide CRISPR-Cas9 forward screening, we identified 3'-phosphoadenosine 5'-phosphosulfate (PAPS) transporter 1 (PAPST1) as an essential factor for SBV infection. PAPST1 is a sulfotransferase involved in heparan sulfate proteoglycan synthesis encoded by the solute carrier family 35 member B2 gene (SLC35B2). SBV cell surface attachment and entry were largely reduced upon the knockout of SLC35B2, whereas the reconstitution of SLC35B2 in these cells fully restored their susceptibility to SBV infection. Furthermore, treatment of cells with heparinase diminished infection with SBV, confirming that heparan sulfate plays an important role in cell attachment and entry, although to various degrees, heparan sulfate was also found to be important to initiate infection by two other bunyaviruses, La Crosse virus and Rift Valley fever virus. Thus, PAPST1-triggered synthesis of cell surface heparan sulfate is required for the efficient replication of SBV and other bunyaviruses.IMPORTANCE SBV is a newly emerging orthobunyavirus (family Peribunyaviridae) that has spread rapidly across Europe since 2011, resulting in substantial economic losses in livestock farming. In this study, we performed unbiased genome-wide CRISPR-Cas9 screening and identified PAPST1, a sulfotransferase encoded by SLC35B2, as a host entry factor for SBV. Consistent with its role in the synthesis of heparan sulfate, we show that this activity is required for efficient infection by SBV. A comparable dependency on heparan sulfate was also observed for La Crosse virus and Rift Valley fever virus, highlighting the importance of heparan sulfate for host cell infection by bunyaviruses. Thus, the present work provides crucial insights into virus-host interactions of important animal and human pathogens.
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Spreafico R, Soriaga LB, Grosse J, Virgin HW, Telenti A. Advances in Genomics for Drug Development. Genes (Basel) 2020; 11:E942. [PMID: 32824125 PMCID: PMC7465049 DOI: 10.3390/genes11080942] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/04/2020] [Accepted: 08/13/2020] [Indexed: 11/16/2022] Open
Abstract
Drug development (target identification, advancing drug leads to candidates for preclinical and clinical studies) can be facilitated by genetic and genomic knowledge. Here, we review the contribution of population genomics to target identification, the value of bulk and single cell gene expression analysis for understanding the biological relevance of a drug target, and genome-wide CRISPR editing for the prioritization of drug targets. In genomics, we discuss the different scope of genome-wide association studies using genotyping arrays, versus exome and whole genome sequencing. In transcriptomics, we discuss the information from drug perturbation and the selection of biomarkers. For CRISPR screens, we discuss target discovery, mechanism of action and the concept of gene to drug mapping. Harnessing genetic support increases the probability of drug developability and approval.
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Affiliation(s)
| | | | | | | | - Amalio Telenti
- Vir Biotechnology, Inc., San Francisco, CA 94158, USA; (R.S.); (L.B.S.); (J.G.); (H.W.V.)
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Tristan CA, Ormanoglu P, Slamecka J, Malley C, Chu PH, Jovanovic VM, Gedik Y, Bonney C, Barnaeva E, Braisted J, Mallanna SK, Dorjsuren D, Iannotti MJ, Voss TC, Michael S, Simeonov A, Singeç I. Robotic High-Throughput Biomanufacturing and Functional Differentiation of Human Pluripotent Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.03.235242. [PMID: 32793899 PMCID: PMC7418713 DOI: 10.1101/2020.08.03.235242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Efficient translation of human induced pluripotent stem cells (hiPSCs) depends on implementing scalable cell manufacturing strategies that ensure optimal self-renewal and functional differentiation. Currently, manual culture of hiPSCs is highly variable and labor-intensive posing significant challenges for high-throughput applications. Here, we established a robotic platform and automated all essential steps of hiPSC culture and differentiation under chemically defined conditions. This streamlined approach allowed rapid and standardized manufacturing of billions of hiPSCs that can be produced in parallel from up to 90 different patient-and disease-specific cell lines. Moreover, we established automated multi-lineage differentiation to generate primary embryonic germ layers and more mature phenotypes such as neurons, cardiomyocytes, and hepatocytes. To validate our approach, we carefully compared robotic and manual cell culture and performed molecular and functional cell characterizations (e.g. bulk culture and single-cell transcriptomics, mass cytometry, metabolism, electrophysiology, Zika virus experiments) in order to benchmark industrial-scale cell culture operations towards building an integrated platform for efficient cell manufacturing for disease modeling, drug screening, and cell therapy. Combining stem cell-based models and non-stop robotic cell culture may become a powerful strategy to increase scientific rigor and productivity, which are particularly important during public health emergencies (e.g. opioid crisis, COVID-19 pandemic).
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Affiliation(s)
- Carlos A. Tristan
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Pinar Ormanoglu
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Jaroslav Slamecka
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Claire Malley
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Pei-Hsuan Chu
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Vukasin M. Jovanovic
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Yeliz Gedik
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Charles Bonney
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Elena Barnaeva
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - John Braisted
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | | | - Dorjbal Dorjsuren
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Michael J. Iannotti
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Ty C. Voss
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Ilyas Singeç
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
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Leier HC, Weinstein JB, Kyle JE, Lee JY, Bramer LM, Stratton KG, Kempthorne D, Navratil AR, Tafesse EG, Hornemann T, Messer WB, Dennis EA, Metz TO, Barklis E, Tafesse FG. A global lipid map defines a network essential for Zika virus replication. Nat Commun 2020; 11:3652. [PMID: 32694525 PMCID: PMC7374707 DOI: 10.1038/s41467-020-17433-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
Zika virus (ZIKV), an arbovirus of global concern, remodels intracellular membranes to form replication sites. How ZIKV dysregulates lipid networks to allow this, and consequences for disease, is poorly understood. Here, we perform comprehensive lipidomics to create a lipid network map during ZIKV infection. We find that ZIKV significantly alters host lipid composition, with the most striking changes seen within subclasses of sphingolipids. Ectopic expression of ZIKV NS4B protein results in similar changes, demonstrating a role for NS4B in modulating sphingolipid pathways. Disruption of sphingolipid biosynthesis in various cell types, including human neural progenitor cells, blocks ZIKV infection. Additionally, the sphingolipid ceramide redistributes to ZIKV replication sites, and increasing ceramide levels by multiple pathways sensitizes cells to ZIKV infection. Thus, we identify a sphingolipid metabolic network with a critical role in ZIKV replication and show that ceramide flux is a key mediator of ZIKV infection.
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Affiliation(s)
- Hans C Leier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
| | - Jules B Weinstein
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, 99352, USA
| | - Joon-Yong Lee
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, 99352, USA
| | - Lisa M Bramer
- Computing and Analytics Division, National Security Directorate, PNNL, Richland, WA, 99352, USA
| | - Kelly G Stratton
- Computing and Analytics Division, National Security Directorate, PNNL, Richland, WA, 99352, USA
| | - Douglas Kempthorne
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
- Center for Diversity and Inclusion, OHSU, Portland, OR, 97239, USA
| | - Aaron R Navratil
- Departments of Chemistry & Biochemistry and Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Endale G Tafesse
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Thorsten Hornemann
- University Zurich and University Hospital Zurich, University of Zurich, Zurich, 8091, Switzerland
| | - William B Messer
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
- Department of Medicine, Division of Infectious Diseases, OHSU, Portland, Oregon, 97239, USA
| | - Edward A Dennis
- Departments of Chemistry & Biochemistry and Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, 99352, USA
| | - Eric Barklis
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA
| | - Fikadu G Tafesse
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University (OHSU), Portland, OR, 97239, USA.
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Li M, Ramage H, Cherry S. Deciphering flavivirus-host interactions using quantitative proteomics. Curr Opin Immunol 2020; 66:90-97. [PMID: 32682290 DOI: 10.1016/j.coi.2020.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/13/2020] [Accepted: 06/16/2020] [Indexed: 01/09/2023]
Abstract
Flaviviruses are a group of important emerging and re-emerging human pathogens that cause worldwide epidemics with thousands of deaths annually. Flaviviruses are small, enveloped, positive-sense, single-stranded RNA viruses that are obligate intracellular pathogens, relying heavily on host cell machinery for productive replication. Proteomic approaches have become an increasingly powerful tool to investigate the mechanisms by which viruses interact with host proteins and manipulate cellular processes to promote infection. Here, we review recent advances in employing quantitative proteomics techniques to improve our understanding of the complex interplay between flaviviruses and host cells. We describe new findings on our understanding of how flaviviruses impact protein-protein interactions, protein-RNA interactions, protein abundance, and post-translational modifications to modulate viral infection.
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Affiliation(s)
- Minghua Li
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Holly Ramage
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Labeau A, Simon-Loriere E, Hafirassou ML, Bonnet-Madin L, Tessier S, Zamborlini A, Dupré T, Seta N, Schwartz O, Chaix ML, Delaugerre C, Amara A, Meertens L. A Genome-Wide CRISPR-Cas9 Screen Identifies the Dolichol-Phosphate Mannose Synthase Complex as a Host Dependency Factor for Dengue Virus Infection. J Virol 2020; 94:e01751-19. [PMID: 31915280 PMCID: PMC7081898 DOI: 10.1128/jvi.01751-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/20/2019] [Indexed: 12/24/2022] Open
Abstract
Dengue virus (DENV) is a mosquito-borne flavivirus responsible for dengue disease, a major human health concern for which no specific therapies are available. Like other viruses, DENV relies heavily on the host cellular machinery for productive infection. In this study, we performed a genome-wide CRISPR-Cas9 screen using haploid HAP1 cells to identify host genes important for DENV infection. We identified DPM1 and -3, two subunits of the endoplasmic reticulum (ER) resident dolichol-phosphate mannose synthase (DPMS) complex, as host dependency factors for DENV and other related flaviviruses, such as Zika virus (ZIKV). The DPMS complex catalyzes the synthesis of dolichol-phosphate mannose (DPM), which serves as mannosyl donor in pathways leading to N-glycosylation, glycosylphosphatidylinositol (GPI) anchor biosynthesis, and C- or O-mannosylation of proteins in the ER lumen. Mutation in the DXD motif of DPM1, which is essential for its catalytic activity, abolished DPMS-mediated DENV infection. Similarly, genetic ablation of ALG3, a mannosyltransferase that transfers mannose to lipid-linked oligosaccharide (LLO), rendered cells poorly susceptible to DENV. We also established that in cells deficient for DPMS activity, viral RNA amplification is hampered and truncated oligosaccharides are transferred to the viral prM and E glycoproteins, affecting their proper folding. Overall, our study provides new insights into the host-dependent mechanisms of DENV infection and supports current therapeutic approaches using glycosylation inhibitors to treat DENV infection.IMPORTANCE Dengue disease, which is caused by dengue virus (DENV), has emerged as the most important mosquito-borne viral disease in humans and is a major global health concern. DENV encodes only few proteins and relies on the host cell machinery to accomplish its life cycle. The identification of the host factors important for DENV infection is needed to propose new targets for antiviral intervention. Using a genome-wide CRISPR-Cas9 screen, we identified DPM1 and -3, two subunits of the DPMS complex, as important host factors for the replication of DENV as well as other related viruses such as Zika virus. We established that DPMS complex plays dual roles during viral infection, both regulating viral RNA replication and promoting viral structural glycoprotein folding/stability. These results provide insights into the host molecules exploited by DENV and other flaviviruses to facilitate their life cycle.
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Affiliation(s)
- Athena Labeau
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | | | - Mohamed-Lamine Hafirassou
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Lucie Bonnet-Madin
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Sarah Tessier
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Alessia Zamborlini
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Thierry Dupré
- Laboratoire de Biochimie, Hôpital Bichat-Claude Bernard, Paris, France
| | - Nathalie Seta
- Laboratoire de Biochimie, Hôpital Bichat-Claude Bernard, Paris, France
| | - Olivier Schwartz
- Institut Pasteur, Virus and Immunity Unit, CNRS-UMR3569, Paris, France
| | - Marie-Laure Chaix
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
- Laboratoire de Virologie et Département des Maladies Infectieuses, Hôpital Saint-Louis, APHP, Paris, France
| | - Constance Delaugerre
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
- Laboratoire de Virologie et Département des Maladies Infectieuses, Hôpital Saint-Louis, APHP, Paris, France
| | - Ali Amara
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Laurent Meertens
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
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Wang S, Zhang Q, Tiwari SK, Lichinchi G, Yau EH, Hui H, Li W, Furnari F, Rana TM. Integrin αvβ5 Internalizes Zika Virus during Neural Stem Cells Infection and Provides a Promising Target for Antiviral Therapy. Cell Rep 2020; 30:969-983.e4. [PMID: 31956073 PMCID: PMC7293422 DOI: 10.1016/j.celrep.2019.11.020] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 10/17/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
We perform a CRISPR-Cas9 genome-wide screen in glioblastoma stem cells and identify integrin αvβ5 as an internalization factor for Zika virus (ZIKV). Expression of αvβ5 is correlated with ZIKV susceptibility in various cells and tropism in developing human cerebral cortex. A blocking antibody against integrin αvβ5, but not αvβ3, efficiently inhibits ZIKV infection. ZIKV binds to cells but fails to internalize when treated with integrin αvβ5-blocking antibody. αvβ5 directly binds to ZIKV virions and activates focal adhesion kinase, which is required for ZIKV infection. Finally, αvβ5 blocking antibody or two inhibitors, SB273005 and cilengitide, reduces ZIKV infection and alleviates ZIKV-induced pathology in human neural stem cells and in mouse brain. Altogether, our findings identify integrin αvβ5 as an internalization factor for ZIKV, providing a promising therapeutic target, as well as two drug candidates for prophylactic use or treatments for ZIKV infections. Wang et al. show that Zika virus (ZIKV) uses integrin αvβ5 to infect neural stem cells. ZIKV infection can be inhibited by αvβ5 blocking antibody or inhibitors, SB273005 and cilengitide, in human neural stem cells and in mouse brain, providing drug candidates for prophylactic use or treatments for ZIKV infections.
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Affiliation(s)
- Shaobo Wang
- Division of Genetics, Department of Pediatrics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego School of Medicine, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Qiong Zhang
- Division of Genetics, Department of Pediatrics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego School of Medicine, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Shashi Kant Tiwari
- Division of Genetics, Department of Pediatrics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego School of Medicine, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Gianluigi Lichinchi
- Division of Genetics, Department of Pediatrics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego School of Medicine, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Edwin H Yau
- Division of Genetics, Department of Pediatrics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego School of Medicine, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Division of Hematology-Oncology, Department of Internal Medicine, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Hui Hui
- Division of Genetics, Department of Pediatrics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego School of Medicine, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Biology, Bioinformatics Program, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Wanyu Li
- Division of Genetics, Department of Pediatrics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego School of Medicine, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Biology, Bioinformatics Program, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Frank Furnari
- Ludwig Institute for Cancer Research, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Pathology, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Tariq M Rana
- Division of Genetics, Department of Pediatrics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego School of Medicine, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Biology, Bioinformatics Program, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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Abstract
Across zoonotic pathogens, RNA viruses are responsible for disproportionate levels of human disease, suffering, and death. Neurotropic RNA viruses (e.g., rabies, Japanese and Eastern Equine Encephalitis, Ebola, West Nile, Powassan) infect the brain and spinal cord, causing meningitis, encephalitis, microcephaly, and Guillain-Barré syndrome. Mechanistic data explaining the molecular mechanisms of these diseases are lacking, and the enclosure of the central nervous system and the associated meninges in bone complicates access for diagnosis, clinical treatment, and research. Here, we discuss new tissue models, imaging methods, and molecular techniques that are changing research aimed at understanding the pathogenesis of neurotropic RNA viruses.
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Affiliation(s)
- Jenna Antonucci
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Lee Gehrke
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
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73
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So RWL, Chung SW, Lau HHC, Watts JJ, Gaudette E, Al-Azzawi ZAM, Bishay J, Lin LTW, Joung J, Wang X, Schmitt-Ulms G. Application of CRISPR genetic screens to investigate neurological diseases. Mol Neurodegener 2019; 14:41. [PMID: 31727120 PMCID: PMC6857349 DOI: 10.1186/s13024-019-0343-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022] Open
Abstract
The adoption of CRISPR-Cas9 technology for functional genetic screens has been a transformative advance. Due to its modular nature, this technology can be customized to address a myriad of questions. To date, pooled, genome-scale studies have uncovered genes responsible for survival, proliferation, drug resistance, viral susceptibility, and many other functions. The technology has even been applied to the functional interrogation of the non-coding genome. However, applications of this technology to neurological diseases remain scarce. This shortfall motivated the assembly of a review that will hopefully help researchers moving in this direction find their footing. The emphasis here will be on design considerations and concepts underlying this methodology. We will highlight groundbreaking studies in the CRISPR-Cas9 functional genetics field and discuss strengths and limitations of this technology for neurological disease applications. Finally, we will provide practical guidance on navigating the many choices that need to be made when implementing a CRISPR-Cas9 functional genetic screen for the study of neurological diseases.
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Affiliation(s)
- Raphaella W L So
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.,Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada
| | - Sai Wai Chung
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Heather H C Lau
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.,Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada
| | - Jeremy J Watts
- Department of Pharmacology & Toxicology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Erin Gaudette
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Zaid A M Al-Azzawi
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Jossana Bishay
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Lilian Tsai-Wei Lin
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.,Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada
| | - Julia Joung
- Departments of Biological Engineering and Brain and Cognitive Science, and McGovern Institute for Brain Research at MIT, Cambridge, MA, 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Xinzhu Wang
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.,Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada
| | - Gerold Schmitt-Ulms
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada.
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Modelling Neurotropic Flavivirus Infection in Human Induced Pluripotent Stem Cell-Derived Systems. Int J Mol Sci 2019; 20:ijms20215404. [PMID: 31671583 PMCID: PMC6862117 DOI: 10.3390/ijms20215404] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/24/2019] [Accepted: 10/29/2019] [Indexed: 02/06/2023] Open
Abstract
Generation of human induced pluripotent stem cells (hiPSCs) and their differentiation into a variety of cells and organoids have allowed setting up versatile, non-invasive, ethically sustainable, and patient-specific models for the investigation of the mechanisms of human diseases, including viral infections and host–pathogen interactions. In this study, we investigated and compared the infectivity and replication kinetics in hiPSCs, hiPSC-derived neural stem cells (NSCs) and undifferentiated neurons, and the effect of viral infection on host innate antiviral responses of representative flaviviruses associated with diverse neurological diseases, i.e., Zika virus (ZIKV), West Nile virus (WNV), and dengue virus (DENV). In addition, we exploited hiPSCs to model ZIKV infection in the embryo and during neurogenesis. The results of this study confirmed the tropism of ZIKV for NSCs, but showed that WNV replicated in these cells with much higher efficiency than ZIKV and DENV, inducing massive cell death. Although with lower efficiency, all flaviviruses could also infect pluripotent stem cells and neurons, inducing similar patterns of antiviral innate immune response gene expression. While showing the usefulness of hiPSC-based infection models, these findings suggest that additional virus-specific mechanisms, beyond neural tropism, are responsible for the peculiarities of disease phenotype in humans.
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Chasing Intracellular Zika Virus Using Proteomics. Viruses 2019; 11:v11090878. [PMID: 31546825 PMCID: PMC6783930 DOI: 10.3390/v11090878] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 12/11/2022] Open
Abstract
Flaviviruses are the most medically relevant group of arboviruses causing a wide range of diseases in humans and are associated with high mortality and morbidity, as such posing a major health concern. Viruses belonging to this family can be endemic (e.g., dengue virus), but can also cause fulminant outbreaks (e.g., West Nile virus, Japanese encephalitis virus and Zika virus). Intense research efforts in the past decades uncovered shared fundamental strategies used by flaviviruses to successfully replicate in their respective hosts. However, the distinct features contributing to the specific host and tissue tropism as well as the pathological outcomes unique to each individual flavivirus are still largely elusive. The profound footprint of individual viruses on their respective hosts can be investigated using novel technologies in the field of proteomics that have rapidly developed over the last decade. An unprecedented sensitivity and throughput of mass spectrometers, combined with the development of new sample preparation and bioinformatics analysis methods, have made the systematic investigation of virus-host interactions possible. Furthermore, the ability to assess dynamic alterations in protein abundances, protein turnover rates and post-translational modifications occurring in infected cells now offer the unique possibility to unravel complex viral perturbations induced in the infected host. In this review, we discuss the most recent contributions of mass spectrometry-based proteomic approaches in flavivirus biology with a special focus on Zika virus, and their basic and translational potential and implications in understanding and characterizing host responses to arboviral infections.
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