151
|
Lane-Reticker SK, Manguso RT, Haining WN. Pooled in vivo screens for cancer immunotherapy target discovery. Immunotherapy 2019; 10:167-170. [PMID: 29370725 DOI: 10.2217/imt-2017-0164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Sarah K Lane-Reticker
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Broad Institute of Harvard & Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Robert T Manguso
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Broad Institute of Harvard & Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - W Nicholas Haining
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Broad Institute of Harvard & Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Division of Pediatric Hematology & Oncology, Children's Hospital, Boston, MA 02115, USA
| |
Collapse
|
152
|
An RNA-centric dissection of host complexes controlling flavivirus infection. Nat Microbiol 2019; 4:2369-2382. [PMID: 31384002 PMCID: PMC6879806 DOI: 10.1038/s41564-019-0518-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/23/2019] [Indexed: 12/26/2022]
Abstract
Flaviviruses including dengue virus (DENV) and Zika virus (ZIKV) cause significant human disease. Co-opting cellular factors for viral translation and viral genome replication at the endoplasmic reticulum (ER) is a shared replication strategy, despite different clinical outcomes. While the protein products of these viruses have been studied in depth, how the RNA genomes operate inside human cells is poorly understood. Using comprehensive identification of RNA binding proteins by mass spectrometry (ChIRP-MS), we took an RNA-centric viewpoint of flaviviral infection and identified several hundred proteins associated with both DENV and ZIKV genomic RNA in human cells. Genome-scale knockout screens assigned putative functional relevance to the RNA-protein interactions observed by ChIRP-MS. The ER-localized RNA binding proteins vigilin and RRBP1 directly bound viral RNA and each acted at distinct stages in the life cycle of flaviviruses. Thus, this versatile strategy can elucidate features of human biology that control pathogenesis of clinically relevant viruses.
Collapse
|
153
|
A CRISPR Activation Screen Identifies Genes That Protect against Zika Virus Infection. J Virol 2019; 93:JVI.00211-19. [PMID: 31142663 DOI: 10.1128/jvi.00211-19] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/22/2019] [Indexed: 02/05/2023] Open
Abstract
Zika virus (ZIKV) is an arthropod-borne emerging pathogen causing febrile illness. ZIKV is associated Guillain-Barré syndrome and other neurological complications. Infection during pregnancy is associated with pregnancy complications and developmental and neurological abnormalities collectively defined as congenital Zika syndrome. There is still no vaccine or specific treatment for ZIKV infection. To identify host factors that can rescue cells from ZIKV infection, we used a genome-scale CRISPR activation screen. Our highly ranking hits included a short list of interferon-stimulated genes (ISGs) previously reported to have antiviral activity. Validation of the screen results highlighted interferon lambda 2 (IFN-λ2) and interferon alpha-inducible protein 6 (IFI6) as genes providing high levels of protection from ZIKV. Activation of these genes had an effect on an early stage in viral infection. In addition, infected cells expressing single guide RNAs (sgRNAs) for both of these genes displayed lower levels of cell death than did the controls. Furthermore, the identified genes were significantly induced in ZIKV-infected placenta explants. Thus, these results highlight a set of ISGs directly relevant for rescuing cells from ZIKV infection or its associated cell death and substantiate CRISPR activation screens as a tool to identify host factors impeding pathogen infection.IMPORTANCE Zika virus (ZIKV) is an emerging vector-borne pathogen causing a febrile disease. ZIKV infection might also trigger Guillain-Barré syndrome, neuropathy, and myelitis. Vertical transmission of ZIKV can cause fetus demise, stillbirth, or severe congenital abnormalities and neurological complications. There is no vaccine or specific antiviral treatment against ZIKV. We used a genome-wide CRISPR activation screen, where genes are activated from their native promoters to identify host cell factors that protect cells from ZIKV infection or associated cell death. The results provide a better understanding of key host factors that protect cells from ZIKV infection and might assist in identifying novel antiviral targets.
Collapse
|
154
|
Sayed S, Paszkowski-Rogacz M, Schmitt LT, Buchholz F. CRISPR/Cas9 as a tool to dissect cancer mutations. Methods 2019; 164-165:36-48. [PMID: 31078796 DOI: 10.1016/j.ymeth.2019.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 12/26/2022] Open
Abstract
The CRISPR/Cas9 system is transforming many biomedical disciplines, including cancer research. Through its flexible programmability and efficiency to induce DNA double strand breaks it has become straightforward to introduce cancer mutations into cells in vitro and/or in vivo. However, not all mutations contribute equally to tumorigenesis and distinguishing essential mutations for tumor growth and survival from biologically inert mutations is cumbersome. Here we present a method to screen for the functional relevance of mutations in high throughput in established cancer cell lines. We employ the CRISPR/Cas9 system to probe cancer vulnerabilities in a colorectal carcinoma cell line in an attempt to identify novel cancer driver mutations. We designed 100 high quality sgRNAs that are able to specifically cleave mutations present in the colorectal carcinoma cell line RKO. An all-in-one lentiviral library harboring these sgRNAs was then generated and used in a pooled screen to probe possible growth dependencies on these mutations. Genomic DNA at different time points were collected, the sgRNA cassettes were PCR amplified, purified and sgRNA counts were quantified by means of deep sequencing. The analysis revealed two sgRNAs targeting the same mutation (UTP14A: S99delS) to be depleted over time in RKO cells. Validation and characterization confirmed that the inactivation of this mutation impairs cell growth, nominating UTP14A: S99delS as a putative driver mutation in RKO cells. Overall, our approach demonstrates that the CRISPR/Cas9 system is a powerful tool to functionally dissect cancer mutations at large-scale.
Collapse
Affiliation(s)
- Shady Sayed
- Carl Gustav Carus Faculty of Medicine, UCC, Section Medical Systems Biology, TU Dresden, Germany; National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Carl Gustav Carus Faculty of Medicine, UCC, Section Medical Systems Biology, TU Dresden, Germany
| | - Lukas Theo Schmitt
- Carl Gustav Carus Faculty of Medicine, UCC, Section Medical Systems Biology, TU Dresden, Germany
| | - Frank Buchholz
- Carl Gustav Carus Faculty of Medicine, UCC, Section Medical Systems Biology, TU Dresden, Germany; National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| |
Collapse
|
155
|
Barrows NJ, Anglero-Rodriguez Y, Kim B, Jamison SF, Le Sommer C, McGee CE, Pearson JL, Dimopoulos G, Ascano M, Bradrick SS, Garcia-Blanco MA. Dual roles for the ER membrane protein complex in flavivirus infection: viral entry and protein biogenesis. Sci Rep 2019; 9:9711. [PMID: 31273220 PMCID: PMC6609633 DOI: 10.1038/s41598-019-45910-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/27/2019] [Indexed: 12/16/2022] Open
Abstract
Hundreds of cellular host factors are required to support dengue virus infection, but their identity and roles are incompletely characterized. Here, we identify human host dependency factors required for efficient dengue virus-2 (DENV2) infection of human cells. We focused on two, TTC35 and TMEM111, which we previously demonstrated to be required for yellow fever virus (YFV) infection and others subsequently showed were also required by other flaviviruses. These proteins are components of the human endoplasmic reticulum membrane protein complex (EMC), which has roles in ER-associated protein biogenesis and lipid metabolism. We report that DENV, YFV and Zika virus (ZIKV) infections were strikingly inhibited, while West Nile virus infection was unchanged, in cells that lack EMC subunit 4. Furthermore, targeted depletion of EMC subunits in live mosquitoes significantly reduced DENV2 propagation in vivo. Using a novel uncoating assay, which measures interactions between host RNA-binding proteins and incoming viral RNA, we show that EMC is required at or prior to virus uncoating. Importantly, we uncovered a second and important role for the EMC. The complex is required for viral protein accumulation in a cell line harboring a ZIKV replicon, indicating that EMC participates in the complex process of viral protein biogenesis.
Collapse
Affiliation(s)
- Nicholas J Barrows
- Department of Microbiology and Molecular Genetics, and Center for RNA Biology, Duke University, Durham, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, USA
| | - Yesseinia Anglero-Rodriguez
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Byungil Kim
- Department of Biochemistry, Vanderbilt University, Nashville, USA
| | - Sharon F Jamison
- Department of Microbiology and Molecular Genetics, and Center for RNA Biology, Duke University, Durham, USA
| | - Caroline Le Sommer
- Department of Microbiology and Molecular Genetics, and Center for RNA Biology, Duke University, Durham, USA
| | | | - James L Pearson
- Department of Microbiology and Molecular Genetics, and Center for RNA Biology, Duke University, Durham, USA
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Manuel Ascano
- Department of Biochemistry, Vanderbilt University, Nashville, USA
| | - Shelton S Bradrick
- Department of Microbiology and Molecular Genetics, and Center for RNA Biology, Duke University, Durham, USA. .,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, USA.
| | - Mariano A Garcia-Blanco
- Department of Microbiology and Molecular Genetics, and Center for RNA Biology, Duke University, Durham, USA. .,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, USA. .,Programme of Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| |
Collapse
|
156
|
Xiong L, Zhang L, Yang Y, Li N, Lai W, Wang F, Zhu X, Wang T. ER complex proteins are required for rhodopsin biosynthesis and photoreceptor survival in Drosophila and mice. Cell Death Differ 2019; 27:646-661. [PMID: 31263175 PMCID: PMC7206144 DOI: 10.1038/s41418-019-0378-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 12/17/2022] Open
Abstract
Defective rhodopsin homeostasis is one of the major causes of retinal degeneration, including the disease Retinitis pigmentosa. To identify cellular factors required for the biosynthesis of rhodopsin, we performed a genome-wide genetic screen in Drosophila for mutants with reduced levels of rhodopsin. We isolated loss-of-function alleles in endoplasmic reticulum membrane protein complex 3 (emc3), emc5, and emc6, each of which exhibited defective phototransduction and photoreceptor cell degeneration. EMC3, EMC5, and EMC6 were essential for rhodopsin synthesis independent of the ER associated degradation (ERAD) pathway, which eliminates misfolded proteins. We generated null mutations for all EMC subunits, and further demonstrated that different EMC subunits play roles in different cellular functions. Conditional knockout of the Emc3 gene in mice led to mislocalization of rhodopsin protein and death of cone and rod photoreceptor cells. These data indicate conserved roles for EMC subunits in maintaining rhodopsin homeostasis and photoreceptor function, and suggest that retinal degeneration may also be caused by defects in early biosynthesis of rhodopsin.
Collapse
Affiliation(s)
- Liangyao Xiong
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing, 100871, China.,National Institute of Biological Sciences, Beijing, 102206, China
| | - Lin Zhang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
| | - Yeming Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
| | - Na Li
- Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Wenjia Lai
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Fengchao Wang
- National Institute of Biological Sciences, Beijing, 102206, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100871, China
| | - Xianjun Zhu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China. .,Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China. .,Chinese Academy of Sciences Sichuan Translational Medicine Hospital, Chengdu, China. .,Department of Ophthalmology, First People's Hospital of Shangqiu, Shangqiu, Henan, China.
| | - Tao Wang
- National Institute of Biological Sciences, Beijing, 102206, China. .,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100871, China.
| |
Collapse
|
157
|
Kiblawi S, Chasman D, Henning A, Park E, Poon H, Gould M, Ahlquist P, Craven M. Augmenting subnetwork inference with information extracted from the scientific literature. PLoS Comput Biol 2019; 15:e1006758. [PMID: 31246951 PMCID: PMC6619809 DOI: 10.1371/journal.pcbi.1006758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/10/2019] [Accepted: 01/04/2019] [Indexed: 11/20/2022] Open
Abstract
Many biological studies involve either (i) manipulating some aspect of a cell or its environment and then simultaneously measuring the effect on thousands of genes, or (ii) systematically manipulating each gene and then measuring the effect on some response of interest. A common challenge that arises in these studies is to explain how genes identified as relevant in the given experiment are organized into a subnetwork that accounts for the response of interest. The task of inferring a subnetwork is typically dependent on the information available in publicly available, structured databases, which suffer from incompleteness. However, a wealth of potentially relevant information resides in the scientific literature, such as information about genes associated with certain concepts of interest, as well as interactions that occur among various biological entities. We contend that by exploiting this information, we can improve the explanatory power and accuracy of subnetwork inference in multiple applications. Here we propose and investigate several ways in which information extracted from the scientific literature can be used to augment subnetwork inference. We show that we can use literature-extracted information to (i) augment the set of entities identified as being relevant in a subnetwork inference task, (ii) augment the set of interactions used in the process, and (iii) support targeted browsing of a large inferred subnetwork by identifying entities and interactions that are closely related to concepts of interest. We use this approach to uncover the pathways involved in interactions between a virus and a host cell, and the pathways that are regulated by a transcription factor associated with breast cancer. Our experimental results demonstrate that these approaches can provide more accurate and more interpretable subnetworks. Integer program code, background network data, and pathfinding code are available at https://github.com/Craven-Biostat-Lab/subnetwork_inference There is a multitude of publicly available databases that contain information about biological entities (i.e., genes, proteins, and other small molecules) as well as information about how these entities interact together. However, these databases are often incomplete. There is a wealth of information present in the text of the scientific literature that is not yet available in these databases. Using tools that mine the scientific literature we are able to extract some of this potentially relevant information. In this work we show how we can use publicly available databases in conjunction with the information extracted from the scientific literature to infer the networks that are involved in specific biological processes, such as viral replication and cancer tumor growth.
Collapse
Affiliation(s)
- Sid Kiblawi
- Department of Computer Sciences, University of Wisconsin, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI, USA
| | - Amanda Henning
- Department of Oncology, University of Wisconsin, Madison, WI, USA
| | - Eunju Park
- Institute for Molecular Virology, University of Wisconsin, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | | | - Michael Gould
- Department of Oncology, University of Wisconsin, Madison, WI, USA
| | - Paul Ahlquist
- Institute for Molecular Virology, University of Wisconsin, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
- Howard Hughes Medical Institute, University of Wisconsin, Madison, WI, USA
| | - Mark Craven
- Department of Computer Sciences, University of Wisconsin, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
- * E-mail:
| |
Collapse
|
158
|
Cellular Interleukin Enhancer-Binding Factor 2, ILF2, Inhibits Japanese Encephalitis Virus Replication In Vitro. Viruses 2019; 11:v11060559. [PMID: 31212927 PMCID: PMC6631381 DOI: 10.3390/v11060559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/01/2019] [Accepted: 06/16/2019] [Indexed: 12/29/2022] Open
Abstract
Japanese encephalitis virus (JEV) is a zoonotic mosquito-borne flavivirus which is the leading causative agent of viral encephalitis in endemic regions. JEV NS3 is a component of the viral replicase complex and is a multifunctional protein. In this study, interleukin enhancer-binding factor 2 (ILF2) is identified as a novel cellular protein interacting with NS3 through co-immunoprecipitation assay and LC-MS/MS. The expression of ILF2 is decreased in JEV-infected human embryonic kidney (293T) cells. The knockdown of endogenous ILF2 by special short hairpin RNA (shRNA) positively regulates JEV propagation, whereas the overexpression of ILF2 results in a significantly reduced JEV genome synthesis. Further analysis revealed that the knockdown of ILF2 positively regulates viral replication by JEV replicon system studies. These results suggest that ILF2 may act as a potential antiviral agent against JEV infection.
Collapse
|
159
|
Abstract
Abstract
The development of clustered regularly interspaced short-palindromic repeat (CRISPR)-Cas systems for genome editing has transformed the way life science research is conducted and holds enormous potential for the treatment of disease as well as for many aspects of biotechnology. Here, I provide a personal perspective on the development of CRISPR-Cas9 for genome editing within the broader context of the field and discuss our work to discover novel Cas effectors and develop them into additional molecular tools. The initial demonstration of Cas9-mediated genome editing launched the development of many other technologies, enabled new lines of biological inquiry, and motivated a deeper examination of natural CRISPR-Cas systems, including the discovery of new types of CRISPR-Cas systems. These new discoveries in turn spurred further technological developments. I review these exciting discoveries and technologies as well as provide an overview of the broad array of applications of these technologies in basic research and in the improvement of human health. It is clear that we are only just beginning to unravel the potential within microbial diversity, and it is quite likely that we will continue to discover other exciting phenomena, some of which it may be possible to repurpose as molecular technologies. The transformation of mysterious natural phenomena to powerful tools, however, takes a collective effort to discover, characterize, and engineer them, and it has been a privilege to join the numerous researchers who have contributed to this transformation of CRISPR-Cas systems.
Collapse
|
160
|
Campos RK, Garcia-Blanco MA, Bradrick SS. Roles of Pro-viral Host Factors in Mosquito-Borne Flavivirus Infections. Curr Top Microbiol Immunol 2019; 419:43-67. [PMID: 28688087 DOI: 10.1007/82_2017_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Identification and analysis of viral host factors is a growing area of research which aims to understand the how viruses molecularly interface with the host cell. Investigations into flavivirus-host interactions has led to new discoveries in viral and cell biology, and will potentially bolster strategies to control the important diseases caused by these pathogens. Here, we address the current knowledge of prominent host factors required for the flavivirus life-cycle and mechanisms by which they promote infection.
Collapse
Affiliation(s)
- Rafael K Campos
- Department of Molecular Genetics and Microbiology, Center for RNA Biology, Duke University, Durham, NC, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA. .,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| | - Shelton S Bradrick
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| |
Collapse
|
161
|
Affiliation(s)
- Martin R Pool
- School of Biological Sciences, Faculty of Biology Medicine and Health, Health Innovation Manchester, University of Manchester, Manchester, UK.
| | - Ilaria Russo
- Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA.
| |
Collapse
|
162
|
Genome-wide CRISPR screen for Zika virus resistance in human neural cells. Proc Natl Acad Sci U S A 2019; 116:9527-9532. [PMID: 31019072 DOI: 10.1073/pnas.1900867116] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Zika virus (ZIKV) is a neurotropic and neurovirulent arbovirus that has severe detrimental impact on the developing human fetal brain. To date, little is known about the factors required for ZIKV infection of human neural cells. We identified ZIKV host genes in human pluripotent stem cell (hPSC)-derived neural progenitors (NPs) using a genome-wide CRISPR-Cas9 knockout screen. Mutations of host factors involved in heparan sulfation, endocytosis, endoplasmic reticulum processing, Golgi function, and interferon activity conferred resistance to infection with the Uganda strain of ZIKV and a more recent North American isolate. Host genes essential for ZIKV replication identified in human NPs also provided a low level of protection against ZIKV in isogenic human astrocytes. Our findings provide insights into host-dependent mechanisms for ZIKV infection in the highly vulnerable human NP cells and identify molecular targets for potential therapeutic intervention.
Collapse
|
163
|
Sun N, Petiwala S, Wang R, Lu C, Hu M, Ghosh S, Hao Y, Miller CP, Chung N. Development of drug-inducible CRISPR-Cas9 systems for large-scale functional screening. BMC Genomics 2019; 20:225. [PMID: 30890156 PMCID: PMC6425629 DOI: 10.1186/s12864-019-5601-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/12/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Large-scale genetic screening using CRISPR-Cas9 technology has emerged as a powerful approach to uncover and validate gene functions. The ability to control the timing of genetic perturbation during CRISPR screens will facilitate precise dissection of dynamic and complex biological processes. Here, we report the optimization of a drug-inducible CRISPR-Cas9 system that allows high-throughput gene interrogation with a temporal control. RESULTS We designed multiple drug-inducible sgRNA expression vectors and measured their activities using an EGFP gene disruption assay in 11 human and mouse cell lines. The optimal design allows for a tight and inducible control of gene knockout in vitro, and in vivo during a seven-week-long experiment following hematopoietic reconstitution in mice. We next performed parallel genome-wide loss-of-function screens using the inducible and constitutive CRISPR-Cas9 systems. In proliferation-based dropout screens, these two approaches have similar performance in discriminating essential and nonessential genes. In a more challenging phenotypic assay that requires cytokine stimulation and cell staining, we observed similar sensitivity of the constitutive and drug-induced screening approaches in detecting known hits. Importantly, we demonstrate minimal leakiness of our inducible CRISPR screening platforms in the absence of chemical inducers in large-scale settings. CONCLUSIONS In this study, we have developed a drug-inducible CRISPR-Cas9 system that shows high cleavage efficiency upon induction but low background activity. Using this system, we have achieved inducible gene disruption in a wide range of cell types both in vitro and in vivo. For the first time, we present a systematic side-by-side comparison of constitutive and drug-inducible CRISPR-Cas9 platforms in large-scale functional screens. We demonstrate the tightness and efficiency of our drug-inducible CRISPR-Cas9 system in genome-wide pooled screening. Our design increases the versatility of CRISPR-based genetic screening and represents a significant upgrade on existing functional genomics toolbox.
Collapse
Affiliation(s)
- Ning Sun
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA.
| | - Sakina Petiwala
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - Rui Wang
- AbbVie Cambridge Research Center, 200 Sydney St, Cambridge, MA, 02139, USA
| | - Charles Lu
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - Mufeng Hu
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - Sujana Ghosh
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - Yan Hao
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | | | - Namjin Chung
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA.
| |
Collapse
|
164
|
West Nile Virus-Inclusive Single-Cell RNA Sequencing Reveals Heterogeneity in the Type I Interferon Response within Single Cells. J Virol 2019; 93:JVI.01778-18. [PMID: 30626670 DOI: 10.1128/jvi.01778-18] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/20/2018] [Indexed: 02/08/2023] Open
Abstract
West Nile virus (WNV) is a neurotropic mosquito-borne flavivirus of global importance. Neuroinvasive WNV infection results in encephalitis and can lead to prolonged neurological impairment or death. Type I interferon (IFN-I) is crucial for promoting antiviral defenses through the induction of antiviral effectors, which function to restrict viral replication and spread. However, our understanding of the antiviral response to WNV infection is mostly derived from analysis of bulk cell populations. It is becoming increasingly apparent that substantial heterogeneity in cellular processes exists among individual cells, even within a seemingly homogenous cell population. Here, we present WNV-inclusive single-cell RNA sequencing (scRNA-seq), an approach to examine the transcriptional variation and viral RNA burden across single cells. We observed that only a few cells within the bulk population displayed robust transcription of IFN-β mRNA, and this did not appear to depend on viral RNA abundance within the same cell. Furthermore, we observed considerable transcriptional heterogeneity in the IFN-I response, with genes displaying high unimodal and bimodal expression patterns. Broadly, IFN-stimulated genes negatively correlated with viral RNA abundance, corresponding with a precipitous decline in expression in cells with high viral RNA levels. Altogether, we demonstrated the feasibility and utility of WNV-inclusive scRNA-seq as a high-throughput technique for single-cell transcriptomics and WNV RNA detection. This approach can be implemented in other models to provide insights into the cellular features of protective immunity and identify novel therapeutic targets.IMPORTANCE West Nile virus (WNV) is a clinically relevant pathogen responsible for recurrent epidemics of neuroinvasive disease. Type I interferon is essential for promoting an antiviral response against WNV infection; however, it is unclear how heterogeneity in the antiviral response at the single-cell level impacts viral control. Specifically, conventional approaches lack the ability to distinguish differences across cells with varying viral abundance. The significance of our research is to demonstrate a new technique for studying WNV infection at the single-cell level. We discovered extensive variation in antiviral gene expression and viral abundance across cells. This protocol can be applied to primary cells or in vivo models to better understand the underlying cellular heterogeneity following WNV infection for the development of targeted therapeutic strategies.
Collapse
|
165
|
Hafirassou ML, Meertens L, Umaña-Diaz C, Labeau A, Dejarnac O, Bonnet-Madin L, Kümmerer BM, Delaugerre C, Roingeard P, Vidalain PO, Amara A. A Global Interactome Map of the Dengue Virus NS1 Identifies Virus Restriction and Dependency Host Factors. Cell Rep 2019; 21:3900-3913. [PMID: 29281836 DOI: 10.1016/j.celrep.2017.11.094] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/11/2017] [Accepted: 11/28/2017] [Indexed: 12/25/2022] Open
Abstract
Dengue virus (DENV) infections cause the most prevalent mosquito-borne viral disease worldwide, for which no therapies are available. DENV encodes seven non-structural (NS) proteins that co-assemble and recruit poorly characterized host factors to form the DENV replication complex essential for viral infection. Here, we provide a global proteomic analysis of the human host factors that interact with the DENV NS1 protein. Combined with a functional RNAi screen, this study reveals a comprehensive network of host cellular processes involved in DENV infection and identifies DENV host restriction and dependency factors. We highlight an important role of RACK1 and the chaperonin TRiC (CCT) and oligosaccharyltransferase (OST) complexes during DENV replication. We further show that the OST complex mediates NS1 and NS4B glycosylation, and pharmacological inhibition of its N-glycosylation function strongly impairs DENV infection. In conclusion, our study provides a global interactome of the DENV NS1 and identifies host factors targetable for antiviral therapies.
Collapse
Affiliation(s)
- Mohamed Lamine Hafirassou
- INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Sorbonne Paris Cité, Université Paris Diderot, Hôpital Saint Louis, 75010 Paris, France.
| | - Laurent Meertens
- INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Sorbonne Paris Cité, Université Paris Diderot, Hôpital Saint Louis, 75010 Paris, France
| | - Claudia Umaña-Diaz
- INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Sorbonne Paris Cité, Université Paris Diderot, Hôpital Saint Louis, 75010 Paris, France
| | - Athena Labeau
- INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Sorbonne Paris Cité, Université Paris Diderot, Hôpital Saint Louis, 75010 Paris, France
| | - Ophelie Dejarnac
- INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Sorbonne Paris Cité, Université Paris Diderot, Hôpital Saint Louis, 75010 Paris, France
| | - Lucie Bonnet-Madin
- INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Sorbonne Paris Cité, Université Paris Diderot, Hôpital Saint Louis, 75010 Paris, France
| | - Beate M Kümmerer
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | | | - Philippe Roingeard
- INSERM U966 MAVIVH, Faculté de Médecine, Université de Tours, Tours, France
| | - Pierre-Olivier Vidalain
- Equipe Chimie & Biologie, Modélisation et Immunologie pour la Thérapie, Université Paris Descartes, CNRS UMR 8601, Paris, France
| | - Ali Amara
- INSERM U944, CNRS UMR 7212, Institut Universitaire d'Hématologie, Sorbonne Paris Cité, Université Paris Diderot, Hôpital Saint Louis, 75010 Paris, France.
| |
Collapse
|
166
|
Identification of antiviral roles for the exon-junction complex and nonsense-mediated decay in flaviviral infection. Nat Microbiol 2019; 4:985-995. [PMID: 30833725 PMCID: PMC6533143 DOI: 10.1038/s41564-019-0375-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/18/2019] [Indexed: 12/31/2022]
Abstract
West Nile virus (WNV) is an emerging mosquito-borne flavivirus, related to dengue virus and Zika virus. To gain insight into host pathways involved in WNV infection, we performed a systematic affinity-tag purification mass spectrometry (AP-MS) study to identify 259 WNV-interacting human proteins. RNAi screening revealed 26 genes that both interact with WNV proteins and influence WNV infection. We found that WNV, dengue and Zika virus capsids interact with a conserved subset of proteins that impact infection. These include the exon-junction complex (EJC) recycling factor, PYM1, which is antiviral against all three viruses. The EJC has roles in nonsense-mediated decay (NMD), and we found that both the EJC and NMD are antiviral and the EJC protein RBM8A directly binds WNV RNA. To counteract this, flavivirus infection inhibits NMD and the capsid-PYM1 interaction interferes with EJC protein function and localization. Depletion of PYM1 attenuates RBM8A binding to viral RNA, suggesting that WNV sequesters PYM1 to protect viral RNA from decay. Together, these data suggest a complex interplay between the virus and host in regulating NMD and the EJC.
Collapse
|
167
|
Lu H, Cherepanova NA, Gilmore R, Contessa JN, Lehrman MA. Targeting STT3A-oligosaccharyltransferase with NGI-1 causes herpes simplex virus 1 dysfunction. FASEB J 2019; 33:6801-6812. [PMID: 30811219 DOI: 10.1096/fj.201802044rr] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Herpes simplex virus 1 (HSV-1) is a contagious neurotropic herpesvirus responsible for oral lesions and herpesviral encephalitis. The HSV-1 envelope contains N-glycosylated proteins involved in infection and that are candidate drug targets. NGI-1 is a small-molecule inhibitor of oligosaccharyltransferase (OST) complexes STT3A-OST and STT3B-OST, which catalyze cotranslational and post-translational N-glycosylation, respectively. Because host OSTs attach HSV-1 glycans, NGI-1 might have anti-HSV-1 activity. We evaluated HSV-1 function using NGI-1 and human embryonic kidney 293 knockout lines for OST isoform-specific catalytic and accessory subunits. N-glycosylation of 2 representative envelope proteins (gC and gD) was primarily dependent upon STT3A-OST, but to a large extent replaceable by STT3B-OST. Knockouts impairing STT3A- or STT3B-OST activity, by themselves, did not appreciably affect HSV-1 function (plaque-forming units, normalized to viral particles measured by unglycosylated capsid protein VP5 content). However, with cells lacking STT3B-OST activity (missing the catalytic subunit STT3B or the oxidoreductase subunits magnesium transporter 1/tumor suppressor candidate 3) and thus solely dependent upon STT3A-OST for N-glycosylation, NGI-1 treatment resulted in HSV-1 having cell type-dependent dysfunction (affecting infectivity with Vero cells much more than with the 293 lines). Ablation of post-translational N-glycosylation can therefore make HSV-1 infectivity, and possibly masking of immunogenic peptide epitopes by glycans, highly sensitive to pharmacological inhibition of cotranslational N-glycosylation.-Lu, H., Cherepanova, N. A., Gilmore, R., Contessa, J. N., Lehrman, M. A. Targeting STT3A-oligosaccharyltransferase with NGI-1 causes herpes simplex virus 1 dysfunction.
Collapse
Affiliation(s)
- Hua Lu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Natalia A Cherepanova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Joseph N Contessa
- Department of Therapeutic Radiology and Pharmacology, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Mark A Lehrman
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
168
|
Chitwood PJ, Hegde RS. The Role of EMC during Membrane Protein Biogenesis. Trends Cell Biol 2019; 29:371-384. [PMID: 30826214 DOI: 10.1016/j.tcb.2019.01.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/27/2019] [Accepted: 01/28/2019] [Indexed: 12/11/2022]
Abstract
Ten years ago, high-throughput genetic interaction analyses revealed an abundant and widely conserved protein complex residing in the endoplasmic reticulum (ER) membrane. Dubbed the ER membrane protein complex (EMC), its disruption has since been found to affect wide-ranging processes, including protein trafficking, organelle communication, ER stress, viral maturation, lipid homeostasis, and others. However, its molecular function has remained enigmatic. Recent studies suggest a role for EMC during membrane protein biogenesis. Biochemical reconstitution experiments show that EMC can directly mediate the insertion of transmembrane domains (TMDs) into the lipid bilayer. Given the large proportion of genes encoding membrane proteins, a central role for EMC as a TMD insertion factor can explain its high abundance, wide conservation, and pleiotropic phenotypes.
Collapse
Affiliation(s)
- Patrick J Chitwood
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB20QH, UK
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB20QH, UK.
| |
Collapse
|
169
|
RNA Helicase A Is an Important Host Factor Involved in Dengue Virus Replication. J Virol 2019; 93:JVI.01306-18. [PMID: 30463971 DOI: 10.1128/jvi.01306-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/12/2018] [Indexed: 12/23/2022] Open
Abstract
Dengue virus (DENV) utilizes host factors throughout its life cycle. In this study, we identified RNA helicase A (RHA), a member of the DEAD/H helicase family, as an important host factor of DENV. In response to DENV2 infection, nuclear RHA protein was partially redistributed into the cytoplasm. The short interfering RNA-mediated knockdown of RHA significantly reduced the amounts of infectious viral particles in various cells. The RHA knockdown reduced the multistep viral growth of DENV2 and Japanese encephalitis virus but not Zika virus. Further study showed that the absence of RHA resulted in a reduction of both viral RNA and protein levels, and the data obtained from the reporter replicon assay indicated that RHA does not directly promote viral protein synthesis. RHA bound to the DENV RNA and associated with three nonstructural proteins, including NS1, NS2B3, and NS4B. Further study showed that different domains of RHA mediated its interaction with these viral proteins. The expression of RHA or RHA-K417R mutant protein lacking ATPase/helicase activity in RHA-knockdown cells successfully restored DENV2 replication levels, suggesting that the helicase activity of RHA is dispensable for its proviral effect. Overall, our work reveals that RHA is an important factor of DENV and might serve as a target for antiviral agents.IMPORTANCE Dengue, caused by dengue virus, is a rapidly spreading disease, and currently there are no treatments available. Host factors involved in the viral replication of dengue virus are potential antiviral therapeutic targets. Although RHA has been shown to promote the multiplication of several viruses, such as HIV and adenovirus, its role in the flavivirus family, including dengue virus, Japanese encephalitis virus, and emerging Zika virus, remains elusive. The current study revealed that RHA relocalized into the cytoplasm upon DENV infection and associated with viral RNA and nonstructural proteins, implying that RHA was actively engaged in the viral life cycle. We further provide evidence that RHA promoted the viral yields of DENV2 independent of its helicase activity. These findings demonstrated that RHA is a new host factor required for DENV replication and might serve as a target for antiviral drugs.
Collapse
|
170
|
A Disintegrin and Metalloproteinase 9 Domain (ADAM9) Is a Major Susceptibility Factor in the Early Stages of Encephalomyocarditis Virus Infection. mBio 2019; 10:mBio.02734-18. [PMID: 30723129 PMCID: PMC6428755 DOI: 10.1128/mbio.02734-18] [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] [Indexed: 02/07/2023] Open
Abstract
Encephalomyocarditis virus (EMCV) is a picornavirus that produces lytic infections in murine and human cells. Employing a genome-wide CRISPR-Cas9 knockout screen to find host factors required for EMCV infection, we identified a role for ADAM9 in EMCV infection. CRISPR-mediated deletion of ADAM9 in multiple human cell lines rendered the cells highly resistant to EMCV infection and cell death. Primary fibroblasts from ADAM9 KO mice were also strongly resistant to EMCV infection and cell death. In contrast, ADAM9 KO and WT cells were equally susceptible to infection with other viruses, including the picornavirus Coxsackie virus B. ADAM9 KO cells failed to produce viral progeny when incubated with EMCV. However, bypassing EMCV entry into cells through delivery of viral RNA directly to the cytosol yielded infectious EMCV virions from ADAM9 KO cells, suggesting that ADAM9 is not required for EMCV replication post-entry. These findings establish that ADAM9 is required for the early stage of EMCV infection, likely for virus entry or viral genome delivery to the cytosol.IMPORTANCE Viral myocarditis is a leading cause of death in the United States, contributing to numerous unexplained deaths in people ≤35 years old. Enteroviruses contribute to many cases of human myocarditis. Encephalomyocarditis virus (EMCV) infection causes viral myocarditis in rodent models, but its receptor requirements have not been fully identified. CRISPR-Cas9 screens can identify host dependency factors essential for EMCV infection and enhance our understanding of key events that follow viral infection, potentially leading to new strategies for preventing viral myocarditis. Using a CRISPR-Cas9 screen, we identified a disintegrin and metalloproteinase 9 domain (ADAM9) as a major factor required for the early stages of EMCV infection in both human and murine infection.
Collapse
|
171
|
Carlin AF, Shresta S. Genome-wide approaches to unravelling host-virus interactions in Dengue and Zika infections. Curr Opin Virol 2019; 34:29-38. [PMID: 30576956 PMCID: PMC6476700 DOI: 10.1016/j.coviro.2018.11.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/08/2018] [Accepted: 11/30/2018] [Indexed: 12/16/2022]
Abstract
Genomics approaches are increasingly utilized to probe host-viral interactions and identify mechanisms of viral pathogenesis and host-subversion. Here we review recent studies that utilize Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 screens, transcriptomics and epigenomics to gain insight into Dengue and Zika virus infections in humans. We discuss the benefits and limitations of recently utilized techniques that separate virally infected cells from neighboring uninfected cells to identify the mechanisms by which these viruses regulate host responses. We conclude by discussing how these approaches can best advance our understanding of Dengue and Zika virus pathogenesis in humans.
Collapse
Affiliation(s)
- Aaron F Carlin
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States.
| | - Sujan Shresta
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States; Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA, United States.
| |
Collapse
|
172
|
Abstract
CRISPR technology has opened a new era of genome interrogation and genome engineering. Discovered in bacteria, where it protects against bacteriophage by cleaving foreign nucleic acid sequences, the CRISPR system has been repurposed as an adaptable tool for genome editing and multiple other applications. CRISPR's ease of use, precision, and versatility have led to its widespread adoption, accelerating biomedical research and discovery in human cells and model organisms. Here we review CRISPR-based tools and discuss how they are being applied to decode the genetic circuits that control immune function in health and disease. Genetic variation in immune cells can affect autoimmune disease risk, infectious disease pathogenesis, and cancer immunotherapies. CRISPR provides unprecedented opportunities for functional mechanistic studies of coding and noncoding genome sequence function in immunity. Finally, we discuss the potential of CRISPR technology to engineer synthetic cellular immunotherapies for a wide range of human diseases.
Collapse
Affiliation(s)
- Dimitre R Simeonov
- Biomedical Sciences Graduate Program, University of California, San Francisco, California 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA; .,Diabetes Center, University of California, San Francisco, California 94143, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA; .,Diabetes Center, University of California, San Francisco, California 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California 94720, USA.,Department of Medicine, University of California, San Francisco, California 94143, USA.,Chan Zuckerberg Biohub, San Francisco, California 94158, USA.,UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA
| |
Collapse
|
173
|
Kim J, Koo BK, Yoon KJ. Modeling Host-Virus Interactions in Viral Infectious Diseases Using Stem-Cell-Derived Systems and CRISPR/Cas9 Technology. Viruses 2019; 11:v11020124. [PMID: 30704043 PMCID: PMC6409779 DOI: 10.3390/v11020124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/14/2019] [Accepted: 01/23/2019] [Indexed: 02/06/2023] Open
Abstract
Pathologies induced by viral infections have undergone extensive study, with traditional model systems such as two-dimensional (2D) cell cultures and in vivo mouse models contributing greatly to our understanding of host-virus interactions. However, the technical limitations inherent in these systems have constrained efforts to more fully understand such interactions, leading to a search for alternative in vitro systems that accurately recreate in vivo physiology in order to advance the study of viral pathogenesis. Over the last decade, there have been significant technological advances that have allowed researchers to more accurately model the host environment when modeling viral pathogenesis in vitro, including induced pluripotent stem cells (iPSCs), adult stem-cell-derived organoid culture systems and CRISPR/Cas9-mediated genome editing. Such technological breakthroughs have ushered in a new era in the field of viral pathogenesis, where previously challenging questions have begun to be tackled. These include genome-wide analysis of host-virus crosstalk, identification of host factors critical for viral pathogenesis, and the study of viral pathogens that previously lacked a suitable platform, e.g., noroviruses, rotaviruses, enteroviruses, adenoviruses, and Zika virus. In this review, we will discuss recent advances in the study of viral pathogenesis and host-virus crosstalk arising from the use of iPSC, organoid, and CRISPR/Cas9 technologies.
Collapse
Affiliation(s)
- Jihoon Kim
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| | - Ki-Jun Yoon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| |
Collapse
|
174
|
Volkmar N, Thezenas ML, Louie SM, Juszkiewicz S, Nomura DK, Hegde RS, Kessler BM, Christianson JC. The ER membrane protein complex promotes biogenesis of sterol-related enzymes maintaining cholesterol homeostasis. J Cell Sci 2019; 132:jcs.223453. [PMID: 30578317 PMCID: PMC6362398 DOI: 10.1242/jcs.223453] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/03/2018] [Indexed: 12/24/2022] Open
Abstract
The eukaryotic endoplasmic reticulum (ER) membrane contains essential complexes that oversee protein biogenesis and lipid metabolism, impacting nearly all aspects of cell physiology. The ER membrane protein complex (EMC) is a newly described transmembrane domain (TMD) insertase linked with various phenotypes, but whose clients and cellular responsibilities remain incompletely understood. We report that EMC deficiency limits the cellular boundaries defining cholesterol tolerance, reflected by diminished viability with limiting or excessive extracellular cholesterol. Lipidomic and proteomic analyses revealed defective biogenesis and concomitant loss of the TMD-containing ER-resident enzymes sterol-O-acyltransferase 1 (SOAT1) and squalene synthase (SQS, also known as FDFT1), which serve strategic roles in the adaptation of cells to changes in cholesterol availability. Insertion of the weakly hydrophobic tail-anchor (TA) of SQS into the ER membrane by the EMC ensures sufficient flux through the sterol biosynthetic pathway while biogenesis of polytopic SOAT1 promoted by the EMC provides cells with the ability to store free cholesterol as inert cholesteryl esters. By facilitating insertion of TMDs that permit essential mammalian sterol-regulating enzymes to mature accurately, the EMC is an important biogenic determinant of cellular robustness to fluctuations in cholesterol availability. This article has an associated First Person interview with the first author of the paper. Highlighted Article: The ER membrane protein complex promotes biogenesis of key membrane-bound enzymes responsible for regulation of cholesterol biosynthesis and storage, an important determinant of mammalian cell viability.
Collapse
Affiliation(s)
- Norbert Volkmar
- Ludwig Institute for Cancer Research, University of Oxford, ORCRB, Headington, Oxford, OX3 7DQ, UK
| | - Maria-Laetitia Thezenas
- Target Discovery Institute (TDI) Mass Spectrometry Laboratory, Nuffield Department of Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Sharon M Louie
- Dept. of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California-Berkeley, Berkeley, CA, 94720, USA
| | - Szymon Juszkiewicz
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Daniel K Nomura
- Dept. of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California-Berkeley, Berkeley, CA, 94720, USA
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Benedikt M Kessler
- Target Discovery Institute (TDI) Mass Spectrometry Laboratory, Nuffield Department of Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - John C Christianson
- Ludwig Institute for Cancer Research, University of Oxford, ORCRB, Headington, Oxford, OX3 7DQ, UK .,Oxford Centre for Translational Myeloma Research, NDORMS, University of Oxford, Botnar Research Centre, Headington, Oxford, OX3 7LD, UK
| |
Collapse
|
175
|
Petrova E, Gracias S, Beauclair G, Tangy F, Jouvenet N. Uncovering Flavivirus Host Dependency Factors through a Genome-Wide Gain-of-Function Screen. Viruses 2019; 11:v11010068. [PMID: 30650657 PMCID: PMC6356745 DOI: 10.3390/v11010068] [Citation(s) in RCA: 15] [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: 12/14/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 01/14/2023] Open
Abstract
Flaviviruses, such as dengue (DENV), West Nile (WNV), yellow fever (YFV) and Zika (ZIKV) viruses, are mosquito-borne pathogens that present a major risk to global public health. To identify host factors that promote flavivirus replication, we performed a genome-wide gain-of-function cDNA screen for human genes that enhance the replication of flavivirus reporter particles in human cells. The screen recovered seventeen potential host proteins that promote viral replication, including the previously known dolichyl-diphosphooligosaccharide--protein glycosyltransferase non-catalytic subunit (DDOST). Using silencing approaches, we validated the role of four candidates in YFV and WNV replication: ribosomal protein L19 (RPL19), ribosomal protein S3 (RPS3), DDOST and importin 9 (IPO9). Applying a panel of virological, biochemical and microscopic methods, we validated further the role of RPL19 and DDOST as host factors required for optimal replication of YFV, WNV and ZIKV. The genome-wide gain-of-function screen is thus a valid approach to advance our understanding of flavivirus replication.
Collapse
Affiliation(s)
- Evgeniya Petrova
- Viral Genomics and Vaccination Unit, UMR3569 CNRS, Virology department, Institut Pasteur, 75015 Paris, France.
| | - Ségolène Gracias
- Viral Genomics and Vaccination Unit, UMR3569 CNRS, Virology department, Institut Pasteur, 75015 Paris, France.
| | - Guillaume Beauclair
- Viral Genomics and Vaccination Unit, UMR3569 CNRS, Virology department, Institut Pasteur, 75015 Paris, France.
| | - Frédéric Tangy
- Viral Genomics and Vaccination Unit, UMR3569 CNRS, Virology department, Institut Pasteur, 75015 Paris, France.
| | - Nolwenn Jouvenet
- Viral Genomics and Vaccination Unit, UMR3569 CNRS, Virology department, Institut Pasteur, 75015 Paris, France.
| |
Collapse
|
176
|
V'kovski P, Gerber M, Kelly J, Pfaender S, Ebert N, Braga Lagache S, Simillion C, Portmann J, Stalder H, Gaschen V, Bruggmann R, Stoffel MH, Heller M, Dijkman R, Thiel V. Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling. eLife 2019; 8:42037. [PMID: 30632963 PMCID: PMC6372286 DOI: 10.7554/elife.42037] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/11/2019] [Indexed: 12/31/2022] Open
Abstract
Positive-sense RNA viruses hijack intracellular membranes that provide niches for viral RNA synthesis and a platform for interactions with host proteins. However, little is known about host factors at the interface between replicase complexes and the host cytoplasm. We engineered a biotin ligase into a coronaviral replication/transcription complex (RTC) and identified >500 host proteins constituting the RTC microenvironment. siRNA-silencing of each RTC-proximal host factor demonstrated importance of vesicular trafficking pathways, ubiquitin-dependent and autophagy-related processes, and translation initiation factors. Notably, detection of translation initiation factors at the RTC was instrumental to visualize and demonstrate active translation proximal to replication complexes of several coronaviruses. Collectively, we establish a spatial link between viral RNA synthesis and diverse host factors of unprecedented breadth. Our data may serve as a paradigm for other positive-strand RNA viruses and provide a starting point for a comprehensive analysis of critical virus-host interactions that represent targets for therapeutic intervention. Coronaviruses can infect the nose and throat and are a main cause of the common cold. Infections are usually mild and short-lived, but sometimes they can turn nasty. In 2002 and 2012, two dangerous new coronaviruses emerged and caused diseases known as SARS and MERS. These viruses caused much more serious symptoms and in some cases proved deadly. The question is, why are some coronaviruses more dangerous than others? Scientists know that the body's response to virus infection can make a difference to whether someone had mild or severe disease. So, to understand why some coronaviruses cause a cold and others kill, they also need to learn how people react to virus infection. Coronaviruses hijack membranes inside cells and turn them into virus factories. Within these factories, the viruses build molecular machinery called replicase complexes to copy their genetic code, which is needed for the next generation of virus particles. The viruses steal and repurpose proteins from their host cell that will assist in the copying process. However, scientists do not yet know which host proteins are essential for the virus to multiply. So, to find out, V’kovski et al. developed a way to tag any host protein that came near the virus factories. The new technique involved attaching an enzyme called a biotin ligase to the replicase complex. This enzyme acts as a molecular label gun, attaching a chemical tag to any protein that comes within ten nanometres. The label gun revealed that more than 500 different proteins come into contact with the replicase complex. To find out what these proteins were doing, the next step was to switch off their genes one by one. This revealed the key cell machinery that coronaviruses hijack when they are replicating. It included the cell's cargo transport system, the waste disposal system, and the protein production system. Using these systems allows the viruses to copy their genetic code next to machines that can turn it straight into viral proteins. These new results provide clues about which proteins viruses actually need from their host cells. They also do not just apply to coronaviruses. Other viruses use similar strategies to complete their infection cycle. These findings could help researchers to understand more generally about how viruses multiply. In the future, this knowledge could lead to new ways to combat virus infections.
Collapse
Affiliation(s)
- Philip V'kovski
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Markus Gerber
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna Kelly
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit, SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Stephanie Pfaender
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sophie Braga Lagache
- Mass Spectrometry and Proteomics Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Cedric Simillion
- Mass Spectrometry and Proteomics Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland.,Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Jasmine Portmann
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Véronique Gaschen
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Michael H Stoffel
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Manfred Heller
- Mass Spectrometry and Proteomics Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Ronald Dijkman
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| |
Collapse
|
177
|
Gorshkov K, Shiryaev SA, Fertel S, Lin YW, Huang CT, Pinto A, Farhy C, Strongin AY, Zheng W, Terskikh AV. Zika Virus: Origins, Pathological Action, and Treatment Strategies. Front Microbiol 2019; 9:3252. [PMID: 30666246 PMCID: PMC6330993 DOI: 10.3389/fmicb.2018.03252] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/14/2018] [Indexed: 01/05/2023] Open
Abstract
The Zika virus (ZIKV) global epidemic prompted the World Health Organization to declare it a 2016 Public Health Emergency of International Concern. The overwhelming experience over the past several years teaches us that ZIKV and the associated neurological complications represent a long-term world-wide challenge to public health. Although the number of ZIKV cases in the Western Hemisphere has dropped since 2016, the need for basic research and anti-ZIKV drug development remains strong. Re-emerging viruses like ZIKV are an ever-present threat in the 21st century where fast transcontinental travel lends itself to viral epidemics. Here, we first present the origin story for ZIKV and review the rapid progress researchers have made toward understanding of the ZIKV pathology and in the design, re-purposing, and testing–particularly in vivo–drug candidates for ZIKV prophylaxis and therapy ZIKV. Quite remarkably, a short, but intensive, drug-repurposing effort has already resulted in several readily available FDA-approved drugs that are capable of effectively combating the virus in infected adult mouse models and, most importantly, in both preventing maternal-fetal transmission and severe microcephaly in newborns in pregnant mouse models.
Collapse
Affiliation(s)
- Kirill Gorshkov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Sergey A Shiryaev
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Sophie Fertel
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Yi-Wen Lin
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Chun-Teng Huang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Antonella Pinto
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Chen Farhy
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Alex Y Strongin
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Alexey V Terskikh
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| |
Collapse
|
178
|
Orchard RC, Sullender ME, Dunlap BF, Balce DR, Doench JG, Virgin HW. Identification of Antinorovirus Genes in Human Cells Using Genome-Wide CRISPR Activation Screening. J Virol 2019; 93:e01324-18. [PMID: 30305350 PMCID: PMC6288323 DOI: 10.1128/jvi.01324-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/27/2018] [Indexed: 12/23/2022] Open
Abstract
Noroviruses (NoVs) are a leading cause of gastroenteritis worldwide, yet host factors that restrict NoV replication are not well understood. Here, we use a CRISPR activation genome-wide screening to identify host genes that can inhibit murine norovirus (MNoV) replication in human cells. Our screens identified with high confidence 49 genes that can inhibit MNoV infection when overexpressed. A significant number of these genes are in interferon and immune regulation signaling networks, but surprisingly, the majority of the genes identified are neither associated with innate or adaptive immunity nor associated with any antiviral activity. Confirmatory studies of eight of the genes validate the initial screening data. Mechanistic studies on TRIM7 demonstrated a conserved role of the molecule in mouse and human cells in restricting MNoV in a step of infection after viral entry. Furthermore, we demonstrate that two isoforms of TRIM7 have differential antiviral activity. Taken together, these data provide a resource for understanding norovirus biology and demonstrate a robust methodology for identifying new antiviral molecules.IMPORTANCE Norovirus is one of the leading causes of food-borne illness worldwide. Despite its prevalence, our understanding of norovirus biology is limited due to the difficulty in growing human norovirus in vitro and a lack of an animal model. Murine norovirus (MNoV) is a model norovirus system because MNoV replicates robustly in cell culture and in mice. To identify host genes that can restrict norovirus replication when overexpressed, we performed genome-wide CRISPR activation screens to induce gene overexpression at the native locus through recruitment of transcriptional activators to individual gene promoters. We found 49 genes that could block murine norovirus replication in human cells. Several of these genes are associated with classical immune signaling pathways, while many of the molecules we identified have not been previously associated with antiviral activity. Our data are a resource for those studying noroviruses, and we provide a robust approach to identify novel antiviral genes.
Collapse
Affiliation(s)
- Robert C Orchard
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Meagan E Sullender
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bria F Dunlap
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dale R Balce
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
179
|
Dengue drug discovery: Progress, challenges and outlook. Antiviral Res 2018; 163:156-178. [PMID: 30597183 DOI: 10.1016/j.antiviral.2018.12.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/22/2018] [Accepted: 12/25/2018] [Indexed: 12/14/2022]
Abstract
In the context of the only available vaccine (DENGVAXIA) that was marketed in several countries, but poses higher risks to unexposed individuals, the development of antivirals for dengue virus (DENV), whilst challenging, would bring significant benefits to public health. Here recent progress in the field of DENV drug discovery made in academic laboratories and industry is reviewed. Characteristics of an ideal DENV antiviral molecule, given the specific immunopathology provoked by this acute viral infection, are described. New chemical classes identified from biochemical, biophysical and phenotypic screens that target viral (especially NS4B) and host proteins, offer promising opportunities for further development. In particular, new methodologies ("omics") can accelerate the discovery of much awaited flavivirus specific inhibitors. Challenges and opportunities in lead identification activities as well as the path to clinical development of dengue drugs are discussed. To galvanize DENV drug discovery, collaborative public-public partnerships and open-access resources will greatly benefit both the DENV research community and DENV patients.
Collapse
|
180
|
Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L, Newton B, Hüttenhain R, Petit MJ, Baum T, Everitt A, Laufman O, Tassetto M, Shales M, Stevenson E, Iglesias GN, Shokat L, Tripathi S, Balasubramaniam V, Webb LG, Aguirre S, Willsey AJ, Garcia-Sastre A, Pollard KS, Cherry S, Gamarnik AV, Marazzi I, Taunton J, Fernandez-Sesma A, Bellen HJ, Andino R, Krogan NJ. Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. Cell 2018; 175:1931-1945.e18. [PMID: 30550790 PMCID: PMC6474419 DOI: 10.1016/j.cell.2018.11.028] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 11/10/2018] [Accepted: 11/19/2018] [Indexed: 01/03/2023]
Abstract
Mosquito-borne flaviviruses, including dengue virus (DENV) and Zika virus (ZIKV), are a growing public health concern. Systems-level analysis of how flaviviruses hijack cellular processes through virus-host protein-protein interactions (PPIs) provides information about their replication and pathogenic mechanisms. We used affinity purification-mass spectrometry (AP-MS) to compare flavivirus-host interactions for two viruses (DENV and ZIKV) in two hosts (human and mosquito). Conserved virus-host PPIs revealed that the flavivirus NS5 protein suppresses interferon stimulated genes by inhibiting recruitment of the transcription complex PAF1C and that chemical modulation of SEC61 inhibits DENV and ZIKV replication in human and mosquito cells. Finally, we identified a ZIKV-specific interaction between NS4A and ANKLE2, a gene linked to hereditary microcephaly, and showed that ZIKV NS4A causes microcephaly in Drosophila in an ANKLE2-dependent manner. Thus, comparative flavivirus-host PPI mapping provides biological insights and, when coupled with in vivo models, can be used to unravel pathogenic mechanisms.
Collapse
Affiliation(s)
- Priya S Shah
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Nichole Link
- Department of Molecular and Human Genetics, and Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA
| | - Gwendolyn M Jang
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tongtong Zhu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jeffrey R Johnson
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - John Von Dollen
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Holly R Ramage
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Satkamp
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Billy Newton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Marine J Petit
- Department of Chemical Engineering, Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Tierney Baum
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Amanda Everitt
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Orly Laufman
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Erica Stevenson
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | | | - Leila Shokat
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Shashank Tripathi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vinod Balasubramaniam
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor, Malaysia
| | - Laurence G Webb
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sebastian Aguirre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - A Jeremy Willsey
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Adolfo Garcia-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katherine S Pollard
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, Institute for Human Genetics, and Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA; Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Ivan Marazzi
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, and Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA.
| |
Collapse
|
181
|
Wang H, Yu Q, Wang L, Li Y, Xie M, Lu Y, Cui Y. Expression of PTEN-long nephritis and its effect on renal inflammation. Exp Ther Med 2018; 17:1405-1411. [PMID: 30680021 DOI: 10.3892/etm.2018.7049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/14/2018] [Indexed: 01/05/2023] Open
Abstract
Based on the important functions of phosphatase and tensin homolog (PTEN)-Long for renal diseases, the present study aimed to investigate the expression of PTEN-Long in patients and mice with nephritis and its effect on nephritis. Expression levels of PTEN-Long in serum of patients with nephritis, renal cell carcinoma (RCC) as well as normal controls, and in serum and renal tissues of mice were measured by western blotting. PTEN-Long knock-in and knock-out mice were constructed via the CRISPR-Cas9 technique. Intraperitoneal injection of lipopolysaccharide+renal homogenate was performed to construct a mouse nephritis model. Mice were divided into control group, model group, knock-in group and knock-out group. A Bio-Plex system was used to detect secretion of serum inflammatory factors. Expression of inflammatory factors in renal tissues of different groups was detected by reverse transcription semi-quantitative polymerase chain reaction. Hematoxylin and eosin staining was used to observe the pathological changes of renal tissue. PTEN-Long was downregulated in patients with nephritis and RCC compared with controls, whereas the expression levels of inflammatory factors were increased. PTEN-long knock-in significantly reduced the serum content and expression levels of tumor necrosis factor (TNF)-α, interleukin (IL)-6, IL-1β and IL-18. PTEN-long knock-out also decreased the expression levels of TNF-α and IL-6 but exhibited no effects on expression of IL-1β and IL-18. Compared with knock-out and model groups, renal tissue inflammation was significantly reduced in knock-in group. The protein level of PTEN-Long was significantly lower in serum than in renal tissue. These findings suggest that PTEN-long can inhibit the progression of nephritis by interacting with inflammatory factors to protect kidney.
Collapse
Affiliation(s)
- Hui Wang
- Institute of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Qingxia Yu
- Critical Care Medicine, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Lin Wang
- Institute of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Yongwei Li
- Institute of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Mao Xie
- Institute of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Youyi Lu
- Institute of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Yupeng Cui
- Institute of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| |
Collapse
|
182
|
Bayat H, Naderi F, Khan AH, Memarnejadian A, Rahimpour A. The Impact of CRISPR-Cas System on Antiviral Therapy. Adv Pharm Bull 2018; 8:591-597. [PMID: 30607331 PMCID: PMC6311650 DOI: 10.15171/apb.2018.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 09/08/2018] [Accepted: 09/29/2018] [Indexed: 12/16/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein nuclease (Cas) is identified as an adaptive immune system in archaea and bacteria. Type II of this system, CRISPR-Cas9, is the most versatile form that has enabled facile and efficient targeted genome editing. Viral infections have serious impacts on global health and conventional antiviral therapies have not yielded a successful solution hitherto. The CRISPR-Cas9 system represents a promising tool for eliminating viral infections. In this review, we highlight 1) the recent progress of CRISPR-Cas technology in decoding and diagnosis of viral outbreaks, 2) its applications to eliminate viral infections in both pre-integration and provirus stages, and 3) various delivery systems that are employed to introduce the platform into target cells.
Collapse
Affiliation(s)
- Hadi Bayat
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Naderi
- Department of Molecular Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Amjad Hayat Khan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | | | - Azam Rahimpour
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
183
|
Zakaria MK, Carletti T, Marcello A. Cellular Targets for the Treatment of Flavivirus Infections. Front Cell Infect Microbiol 2018; 8:398. [PMID: 30483483 PMCID: PMC6240593 DOI: 10.3389/fcimb.2018.00398] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/23/2018] [Indexed: 12/31/2022] Open
Abstract
Classical antiviral therapy targets viral functions, mostly viral enzymes or receptors. Successful examples include precursor herpesvirus drugs, antiretroviral drugs that target reverse transcriptase and protease, influenza virus directed compounds as well as more recent direct antiviral agents (DAA) applied in the treatment of hepatitis C virus (HCV). However, from early times, the possibility of targeting the host cell to contain the infection has frequently re-emerged as an alternative and complementary antiviral strategy. Advantages of this approach include an increased threshold to the emergence of resistance and the possibility to target multiple viruses. Major pitfalls are related to important cellular side effects and cytotoxicity. In this mini-review, the concept of host directed antiviral therapy will be discussed with a focus on the most recent advances in the field of Flaviviruses, a family of important human pathogens for which we do not have antivirals available in the clinics.
Collapse
Affiliation(s)
- Mohammad Khalid Zakaria
- Laboratory of Molecular Virology, International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Tea Carletti
- Laboratory of Molecular Virology, International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Alessandro Marcello
- Laboratory of Molecular Virology, International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| |
Collapse
|
184
|
Rousset F, Cui L, Siouve E, Becavin C, Depardieu F, Bikard D. Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. PLoS Genet 2018; 14:e1007749. [PMID: 30403660 PMCID: PMC6242692 DOI: 10.1371/journal.pgen.1007749] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/19/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022] Open
Abstract
High-throughput genetic screens are powerful methods to identify genes linked to a given phenotype. The catalytic null mutant of the Cas9 RNA-guided nuclease (dCas9) can be conveniently used to silence genes of interest in a method also known as CRISPRi. Here, we report a genome-wide CRISPR-dCas9 screen using a starting pool of ~ 92,000 sgRNAs which target random positions in the chromosome of E. coli. To benchmark our method, we first investigate its utility to predict gene essentiality in the genome of E. coli during growth in rich medium. We could identify 79% of the genes previously reported as essential and demonstrate the non-essentiality of some genes annotated as essential. In addition, we took advantage of the intermediate repression levels obtained when targeting the template strand of genes to show that cells are very sensitive to the expression level of a limited set of essential genes. Our data can be visualized on CRISPRbrowser, a custom web interface available at crispr.pasteur.fr. We then apply the screen to discover E. coli genes required by phages λ, T4 and 186 to kill their host, highlighting the involvement of diverse host pathways in the infection process of the three tested phages. We also identify colanic acid capsule synthesis as a shared resistance mechanism to all three phages. Finally, using a plasmid packaging system and a transduction assay, we identify genes required for the formation of functional λ capsids, thus covering the entire phage cycle. This study demonstrates the usefulness and convenience of pooled genome-wide CRISPR-dCas9 screens in bacteria and paves the way for their broader use as a powerful tool in bacterial genomics. Over the past few years, CRISPR-Cas technologies have emerged as powerful tools to edit genomes and modulate gene expression. They have been applied to perform high-throughput genetic screens with the purpose to understand the function of genes in a systematic manner, but the application of these screens to bacteria have so far remained limited. Here, we present the use of a library of ~92,000 guide RNAs directing the dCas9 protein to silence one by one all the genes in the chromosome of E. coli. To benchmark our method, we first investigate the performance of the technique to identify essential genes, highlighting several non-essential genes also found to be essential by other methods. We then apply our method to detect bacterial genes required by three different bacteriophages to kill E. coli and for the production of functional progeny by phage λ. Our screens highlight previously known and new genetic interactions between phages and their host’s pathways and emphasize the importance of bacterial capsule in the resistance to multiple phages. Altogether, our results demonstrate the usefulness of genome-wide CRISPR-dCas9 screens in bacteria to uncover genes involved in various phenotypes.
Collapse
Affiliation(s)
- François Rousset
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Lun Cui
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - Elise Siouve
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - Christophe Becavin
- Hub Bioinformatique et Biostatistique, Institut Pasteur - C3BI, USR 3756 IP CNRS, Paris, France
| | - Florence Depardieu
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
| | - David Bikard
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- * E-mail:
| |
Collapse
|
185
|
Lino CA, Harper JC, Carney JP, Timlin JA. Delivering CRISPR: a review of the challenges and approaches. Drug Deliv 2018; 25:1234-1257. [PMID: 29801422 PMCID: PMC6058482 DOI: 10.1080/10717544.2018.1474964] [Citation(s) in RCA: 634] [Impact Index Per Article: 105.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/03/2018] [Accepted: 05/07/2018] [Indexed: 12/13/2022] Open
Abstract
Gene therapy has long held promise to correct a variety of human diseases and defects. Discovery of the Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR), the mechanism of the CRISPR-based prokaryotic adaptive immune system (CRISPR-associated system, Cas), and its repurposing into a potent gene editing tool has revolutionized the field of molecular biology and generated excitement for new and improved gene therapies. Additionally, the simplicity and flexibility of the CRISPR/Cas9 site-specific nuclease system has led to its widespread use in many biological research areas including development of model cell lines, discovering mechanisms of disease, identifying disease targets, development of transgene animals and plants, and transcriptional modulation. In this review, we present the brief history and basic mechanisms of the CRISPR/Cas9 system and its predecessors (ZFNs and TALENs), lessons learned from past human gene therapy efforts, and recent modifications of CRISPR/Cas9 to provide functions beyond gene editing. We introduce several factors that influence CRISPR/Cas9 efficacy which must be addressed before effective in vivo human gene therapy can be realized. The focus then turns to the most difficult barrier to potential in vivo use of CRISPR/Cas9, delivery. We detail the various cargos and delivery vehicles reported for CRISPR/Cas9, including physical delivery methods (e.g. microinjection; electroporation), viral delivery methods (e.g. adeno-associated virus (AAV); full-sized adenovirus and lentivirus), and non-viral delivery methods (e.g. liposomes; polyplexes; gold particles), and discuss their relative merits. We also examine several technologies that, while not currently reported for CRISPR/Cas9 delivery, appear to have promise in this field. The therapeutic potential of CRISPR/Cas9 is vast and will only increase as the technology and its delivery improves.
Collapse
Affiliation(s)
- Christopher A. Lino
- Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, NM, USA
| | - Jason C. Harper
- Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, NM, USA
| | - James P. Carney
- Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, NM, USA
| | - Jerilyn A. Timlin
- Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, NM, USA
| |
Collapse
|
186
|
Ting PY, Parker AE, Lee JS, Trussell C, Sharif O, Luna F, Federe G, Barnes SW, Walker JR, Vance J, Gao MY, Klock HE, Clarkson S, Russ C, Miraglia LJ, Cooke MP, Boitano AE, McNamara P, Lamb J, Schmedt C, Snead JL. Guide Swap enables genome-scale pooled CRISPR-Cas9 screening in human primary cells. Nat Methods 2018; 15:941-946. [PMID: 30297964 DOI: 10.1038/s41592-018-0149-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/10/2018] [Indexed: 12/21/2022]
Abstract
CRISPR-Cas9 screening allows genome-wide interrogation of gene function. Currently, to achieve the high and uniform Cas9 expression desirable for screening, one needs to engineer stable and clonal Cas9-expressing cells-an approach that is not applicable in human primary cells. Guide Swap permits genome-scale pooled CRISPR-Cas9 screening in human primary cells by exploiting the unexpected finding that editing by lentivirally delivered, targeted guide RNAs (gRNAs) occurs efficiently when Cas9 is introduced in complex with nontargeting gRNA. We validated Guide Swap in depletion and enrichment screens in CD4+ T cells. Next, we implemented Guide Swap in a model of ex vivo hematopoiesis, and identified known and previously unknown regulators of CD34+ hematopoietic stem and progenitor cell (HSPC) expansion. We anticipate that this platform will be broadly applicable to other challenging cell types, and thus will enable discovery in previously inaccessible but biologically relevant human primary cell systems.
Collapse
Affiliation(s)
- Pamela Y Ting
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Albert E Parker
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Celgene, San Diego, CA, USA
| | - J Scott Lee
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Chris Trussell
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Orzala Sharif
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Fabio Luna
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Glenn Federe
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - S Whitney Barnes
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - John R Walker
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Julie Vance
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mu-Yun Gao
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Heath E Klock
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Merck, Cambridge, MA, USA
| | - Scott Clarkson
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Carsten Russ
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Loren J Miraglia
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Michael P Cooke
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Magenta Therapeutics, Cambridge, MA, USA
| | - Anthony E Boitano
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Magenta Therapeutics, Cambridge, MA, USA
| | - Peter McNamara
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - John Lamb
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Christian Schmedt
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Jennifer L Snead
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA.
| |
Collapse
|
187
|
A one-pot chemoenzymatic synthesis of (2S, 4R)-4-methylproline enables the first total synthesis of antiviral lipopeptide cavinafungin B. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.09.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
188
|
Robinson M, Schor S, Barouch-Bentov R, Einav S. Viral journeys on the intracellular highways. Cell Mol Life Sci 2018; 75:3693-3714. [PMID: 30043139 PMCID: PMC6151136 DOI: 10.1007/s00018-018-2882-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/01/2018] [Accepted: 07/19/2018] [Indexed: 12/24/2022]
Abstract
Viruses are obligate intracellular pathogens that are dependent on cellular machineries for their replication. Recent technological breakthroughs have facilitated reliable identification of host factors required for viral infections and better characterization of the virus-host interplay. While these studies have revealed cellular machineries that are uniquely required by individual viruses, accumulating data also indicate the presence of broadly required mechanisms. Among these overlapping cellular functions are components of intracellular membrane trafficking pathways. Here, we review recent discoveries focused on how viruses exploit intracellular membrane trafficking pathways to promote various stages of their life cycle, with an emphasis on cellular factors that are usurped by a broad range of viruses. We describe broadly required components of the endocytic and secretory pathways, the Endosomal Sorting Complexes Required for Transport pathway, and the autophagy pathway. Identification of such overlapping host functions offers new opportunities to develop broad-spectrum host-targeted antiviral strategies.
Collapse
Affiliation(s)
- Makeda Robinson
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Lane Building, Rm L127, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Stanford Schor
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Lane Building, Rm L127, Stanford, CA, 94305, USA
| | - Rina Barouch-Bentov
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Lane Building, Rm L127, Stanford, CA, 94305, USA
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Lane Building, Rm L127, Stanford, CA, 94305, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
189
|
Romette JL, Prat CM, Gould EA, de Lamballerie X, Charrel R, Coutard B, Fooks AR, Bardsley M, Carroll M, Drosten C, Drexler JF, Günther S, Klempa B, Pinschewer D, Klimkait T, Avsic-Zupanc T, Capobianchi MR, Dicaro A, Ippolito G, Nitsche A, Koopmans M, Reusken C, Gorbalenya A, Raoul H, Bourhy H, Mettenleiter T, Reiche S, Batten C, Sabeta C, Paweska JT, Eropkin M, Zverev V, Hu Z, Mac Cullough S, Mirazimi A, Pradel F, Lieutaud P. The European Virus Archive goes global: A growing resource for research. Antiviral Res 2018; 158:127-134. [PMID: 30059721 PMCID: PMC7127435 DOI: 10.1016/j.antiviral.2018.07.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/21/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry. Within three years, it developed from a consortium of nine European laboratories to encompass associated partners in Africa, Russia, China, Turkey, Germany and Italy. In 2014, the H2020 Research and Innovation Framework Programme (INFRAS projects) provided support for the transformation of the EVA from a European to a global organization (EVAg). The EVAg now operates as a non-profit consortium, with 26 partners and 20 associated partners from 21 EU and non-EU countries. In this paper, we outline the structure, management and goals of the EVAg, to bring to the attention of researchers the wealth of products it can provide and to illustrate how end-users can gain access to these resources. Organisations or individuals who would like to be considered as contributors are invited to contact the EVAg coordinator, Jean-Louis Romette, at jean-louis.romette@univmed.fr.
Collapse
Affiliation(s)
- J L Romette
- Unite des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection), Marseille, France.
| | - C M Prat
- Unite des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection), Marseille, France
| | - E A Gould
- Unite des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection), Marseille, France
| | - X de Lamballerie
- Unite des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection), Marseille, France
| | - R Charrel
- Unite des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection), Marseille, France
| | - B Coutard
- Architectures et Fonctions, des Macromolécules, Biologiques, Marseille, France
| | - A R Fooks
- Animal and Plant Health Agency, Weybridge, United Kingdom
| | - M Bardsley
- Animal and Plant Health Agency, Weybridge, United Kingdom
| | - M Carroll
- Department of Health-Special Pathogens Laboratory, Porton Down, United Kingdom
| | - C Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany
| | - J F Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany
| | - S Günther
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - B Klempa
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - D Pinschewer
- Department of Pathology and Immunology, University of Bales, Switzerland
| | - T Klimkait
- Department of Pathology and Immunology, University of Bales, Switzerland
| | - T Avsic-Zupanc
- Institute of Microbiology and Immunology, Lubljana, Slovenia
| | | | - A Dicaro
- UOC, Istituto Nazionale Malattie Infettive Roma, Italy
| | - G Ippolito
- UOC, Istituto Nazionale Malattie Infettive Roma, Italy
| | - A Nitsche
- Robert Koch Institut, Berlin, Germany
| | - M Koopmans
- ERASMUS Medical Center, Rotterdam, The Netherlands
| | - C Reusken
- ERASMUS Medical Center, Rotterdam, The Netherlands
| | - A Gorbalenya
- Leiden University Medical Center, Leiden, The Netherlands
| | - H Raoul
- Laboratoire Merieux, INSERM, Lyon, France
| | | | - T Mettenleiter
- Friedrich Loeffler Institut, Greifswald-Insel Riems, Germany
| | - S Reiche
- Friedrich Loeffler Institut, Greifswald-Insel Riems, Germany
| | - C Batten
- The Pirbright Institute, Pirbright, United Kingdom
| | - C Sabeta
- Onderstepoort Veterinary Institute, Praetoria, South Africa
| | - J T Paweska
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - M Eropkin
- Research Institute of Influenza, St. Petersburg, Russia
| | - V Zverev
- Mechnikov Scientific Research Institute for Vaccines and Sera, Moscow, Russia
| | - Z Hu
- Wuhan Institute of Virology, Wuhan, China
| | - S Mac Cullough
- Australian Animal Health Laboratory, Geelong, Australia Disease, Johannesburg, South Africa
| | | | - F Pradel
- Fondation Mérieux, réseau GABRIEL, Lyon, France
| | - P Lieutaud
- Unite des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection), Marseille, France
| |
Collapse
|
190
|
Menasche BL, Crisman L, Gulbranson DR, Davis EM, Yu H, Shen J. Fluorescence Activated Cell Sorting (FACS) in Genome-Wide Genetic Screening of Membrane Trafficking. ACTA ACUST UNITED AC 2018; 82:e68. [PMID: 30265447 DOI: 10.1002/cpcb.68] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
About one-third of cellular proteins in eukaryotic cells are localized to membrane-enclosed organelles in the endomembrane system. Trafficking of these membrane proteins (including soluble lumenal proteins) among the organelles is mediated by small sac-like vesicles. Vesicle-mediated membrane trafficking regulates a broad range of biological processes, many of which are still poorly understood at the molecular level. A powerful approach to dissect a vesicle-mediated membrane trafficking pathway is unbiased genome-wide genetic screening, which only recently became possible in mammalian cells with the isolation of haploid human cell lines and the development of CRISPR-Cas9 genome editing. Here, we describe a FACS-based method to select populations of live mutant cells based on the surface levels of endogenous proteins or engineered reporters. Collection of these mutant populations enables subsequent deep sequencing and bioinformatics analysis to identify genes that regulate the trafficking pathway. This method can be readily adapted to genetically dissect a broad range of mammalian membrane trafficking processes using haploid genetics or CRISPR-Cas9 screens. © 2018 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Bridget L Menasche
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado
| | - Lauren Crisman
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado
| | - Daniel R Gulbranson
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado
| | - Eric M Davis
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado
| | - Haijia Yu
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado.,Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jingshi Shen
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado
| |
Collapse
|
191
|
Richardson RB, Ohlson MB, Eitson JL, Kumar A, McDougal MB, Boys IN, Mar KB, De La Cruz-Rivera PC, Douglas C, Konopka G, Xing C, Schoggins JW. A CRISPR screen identifies IFI6 as an ER-resident interferon effector that blocks flavivirus replication. Nat Microbiol 2018; 3:1214-1223. [PMID: 30224801 PMCID: PMC6202210 DOI: 10.1038/s41564-018-0244-1] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 08/13/2018] [Indexed: 11/24/2022]
Abstract
The endoplasmic reticulum (ER) is an architecturally diverse organelle that serves as a membrane source for the replication of multiple viruses. Flaviviruses, including yellow fever virus, West Nile virus, dengue virus and Zika virus, induce unique single-membrane ER invaginations that house the viral replication machinery1. Whether this virus-induced ER remodelling is vulnerable to antiviral pathways is unknown. Here, we show that flavivirus replication at the ER is targeted by the interferon (IFN) response. Through genome-scale CRISPR screening, we uncovered an antiviral mechanism mediated by a functional gene pairing between IFI6 (encoding IFN-α-inducible protein 6), an IFN-stimulated gene cloned over 30 years ago2, and HSPA5, which encodes the ER-resident heat shock protein 70 chaperone BiP. We reveal that IFI6 is an ER-localized integral membrane effector that is stabilized through interactions with BiP. Mechanistically, IFI6 prophylactically protects uninfected cells by preventing the formation of virus-induced ER membrane invaginations. Notably, IFI6 has little effect on other mammalian RNA viruses, including the related Flaviviridae family member hepatitis C virus, which replicates in double-membrane vesicles that protrude outwards from the ER. These findings support a model in which the IFN response is armed with a membrane-targeted effector that discriminately blocks the establishment of virus-specific ER microenvironments that are required for replication. Flavivirus replication at the endoplasmic reticulum (ER) is targeted by the interferon response through blocking of the formation of virus-induced ER membrane invaginations by the interferon-stimulated gene IFI6, encoding an ER-localized integral membrane effector.
Collapse
Affiliation(s)
- R Blake Richardson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Maikke B Ohlson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer L Eitson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ashwani Kumar
- Bioinformatics Core, McDermott Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Matthew B McDougal
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ian N Boys
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Katrina B Mar
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Connor Douglas
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao Xing
- Bioinformatics Core, McDermott Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
192
|
Feng T, Deng L, Lu X, Pan W, Wu Q, Dai J. Ubiquitin-conjugating enzyme UBE2J1 negatively modulates interferon pathway and promotes RNA virus infection. Virol J 2018; 15:132. [PMID: 30157886 PMCID: PMC6114777 DOI: 10.1186/s12985-018-1040-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/10/2018] [Indexed: 12/11/2022] Open
Abstract
Background Viral infection activates innate immune pathways and interferons (IFNs) play a pivotal role in the outcome of a viral infection. Ubiquitin modifications of host and viral proteins significantly influence the progress of virus infection. Ubiquitin-conjugating enzyme E2s (UBE2) have the capacity to determine ubiquitin chain topology and emerge as key mediators of chain assembly. Methods In this study, we screened the functions of 34 E2 genes using an RNAi library during Dengue virus (DENV) infection. RNAi and gene overexpression approaches were used to study the gene function in viral infection and interferon signaling. Results We found that silencing UBE2J1 significantly impaired DENV infection, while overexpression of UBE2J1 enhanced DENV infection. Further studies suggested that type I IFN expression was significantly increased in UBE2J1 silenced cells and decreased in UBE2J1 overexpressed cells. Reporter assay suggested that overexpression of UBE2J1 dramatically suppressed RIG-I directed IFNβ promoter activation. Finally, we have confirmed that UBE2J1 can facilitate the ubiquitination and degradation of transcription factor IFN regulatory factor 3 (IRF3). Conclusion These results suggest that UBE2 family member UBE2J1 can negatively regulate type I IFN expression, thereby promote RNA virus infection. Electronic supplementary material The online version of this article (10.1186/s12985-018-1040-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tingting Feng
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, 199 Ren-ai Road, Suzhou, 215123, People's Republic of China
| | - Lei Deng
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, 199 Ren-ai Road, Suzhou, 215123, People's Republic of China
| | - Xiaochuan Lu
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, 199 Ren-ai Road, Suzhou, 215123, People's Republic of China
| | - Wen Pan
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, 199 Ren-ai Road, Suzhou, 215123, People's Republic of China
| | - Qihan Wu
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai Institute of Planned Parenthood Research, Shanghai, 200032, People's Republic of China.
| | - Jianfeng Dai
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, 199 Ren-ai Road, Suzhou, 215123, People's Republic of China. .,Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai Institute of Planned Parenthood Research, Shanghai, 200032, People's Republic of China.
| |
Collapse
|
193
|
Saiz JC, Oya NJD, Blázquez AB, Escribano-Romero E, Martín-Acebes MA. Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus. Viruses 2018; 10:v10090453. [PMID: 30149598 PMCID: PMC6163279 DOI: 10.3390/v10090453] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/17/2018] [Accepted: 08/22/2018] [Indexed: 12/21/2022] Open
Abstract
Zika virus (ZIKV), a mosquito-borne flavivirus, was an almost neglected pathogen until its introduction in the Americas in 2015, where it has been responsible for a threat to global health, causing a great social and sanitary alarm due to its increased virulence, rapid spread, and an association with severe neurological and ophthalmological complications. Currently, no specific antiviral therapy against ZIKV is available, and treatments are palliative and mainly directed toward the relief of symptoms, such as fever and rash, by administering antipyretics, anti-histamines, and fluids for dehydration. Nevertheless, lately, search for antivirals has been a major aim in ZIKV investigations. To do so, screening of libraries from different sources, testing of natural compounds, and repurposing of drugs with known antiviral activity have allowed the identification of several antiviral candidates directed to both viral (structural proteins and enzymes) and cellular elements. Here, we present an updated review of current knowledge about anti-ZIKV strategies, focusing on host-directed antivirals as a realistic alternative to combat ZIKV infection.
Collapse
Affiliation(s)
- Juan-Carlos Saiz
- Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain.
| | - Nereida Jiménez de Oya
- Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain.
| | - Ana-Belén Blázquez
- Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain.
| | - Estela Escribano-Romero
- Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain.
| | - Miguel A Martín-Acebes
- Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain.
| |
Collapse
|
194
|
Hoffmann HH, Schneider WM, Blomen VA, Scull MA, Hovnanian A, Brummelkamp TR, Rice CM. Diverse Viruses Require the Calcium Transporter SPCA1 for Maturation and Spread. Cell Host Microbe 2018; 22:460-470.e5. [PMID: 29024641 DOI: 10.1016/j.chom.2017.09.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/05/2017] [Accepted: 09/06/2017] [Indexed: 10/18/2022]
Abstract
Respiratory and arthropod-borne viral infections are a global threat due to the lack of effective antivirals and vaccines. A potential strategy is to target host proteins required for viruses but non-essential for the host. To identify such proteins, we performed a genome-wide knockout screen in human haploid cells and identified the calcium pump SPCA1. SPCA1 is required by viruses from the Paramyxoviridae, Flaviviridae, and Togaviridae families, including measles, dengue, West Nile, Zika, and chikungunya viruses. Calcium transport activity is required for SPCA1 to promote virus spread. SPCA1 regulates proteases within the trans-Golgi network that require calcium for their activity and are critical for virus glycoprotein maturation. Consistent with these findings, viral glycoproteins fail to mature in SPCA1-deficient cells preventing viral spread, which is evident even in cells with partial loss of SPCA1. Thus, SPCA1 is an attractive antiviral host target for a broad spectrum of established and emerging viral infections.
Collapse
Affiliation(s)
- H-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - William M Schneider
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Vincent A Blomen
- Biochemistry Division, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Margaret A Scull
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Alain Hovnanian
- INSERM UMR 1163 and Imagine Institute, 75015 Paris, France; Université Paris V Descartes - Sorbonne Paris Cité, 75006 Paris, France; Department of Genetics, Necker Hospital, 75015 Paris, France
| | - Thijn R Brummelkamp
- Biochemistry Division, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Cancer Genomics Centre, 3584 CG Utrecht, The Netherlands
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
195
|
Xu H, Ziani W, Shao J, Doyle-Meyers LA, Russell-Lodrigue KE, Ratterree MS, Veazey RS, Wang X. Impaired Development and Expansion of Germinal Center Follicular Th Cells in Simian Immunodeficiency Virus-Infected Neonatal Macaques. THE JOURNAL OF IMMUNOLOGY 2018; 201:1994-2003. [PMID: 30104244 DOI: 10.4049/jimmunol.1800235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 07/15/2018] [Indexed: 12/16/2022]
Abstract
Germinal center (GC) CD4+ follicular Th (Tfh) cells are critical for cognate B cell help in humoral immune responses to pathogenic infections. Although Tfh cells are expanded or depleted in HIV/SIV-infected adults, the effects of pediatric HIV/SIV infection on Tfh cells remain unclear. In this study, we examined changes in lymphoid follicle formation in lymph nodes focusing on GC Tfh cells, B cell development, and differentiation in SIV-infected neonatal rhesus macaques (Macaca mulatta) compared with age-matched cohorts. Our data showed that follicles and GCs of normal infants rapidly formed in the first few weeks of age, in parallel with increasing GC Tfh cells in various lymphoid tissues. In contrast, GC development and GC Tfh cells were markedly impaired in SIV-infected infants. There was a very low frequency of GC Tfh cells throughout SIV infection in neonates and subsequent infants, accompanied by high viremia, reduction of B cell proliferation/resting memory B cells, and displayed proinflammatory unresponsiveness. These findings indicate neonatal HIV/SIV infection compromises the development of GC Tfh cells, likely contributing to ineffective Ab responses, high viremia, and eventually rapid disease progression to AIDS.
Collapse
Affiliation(s)
- Huanbin Xu
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433
| | - Widade Ziani
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433
| | - Jiasheng Shao
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433
| | - Lara A Doyle-Meyers
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433
| | - Kasi E Russell-Lodrigue
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433
| | - Marion S Ratterree
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433
| | - Ronald S Veazey
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433
| | - Xiaolei Wang
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433
| |
Collapse
|
196
|
Garcia-Moreno M, Järvelin AI, Castello A. Unconventional RNA-binding proteins step into the virus-host battlefront. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1498. [PMID: 30091184 PMCID: PMC7169762 DOI: 10.1002/wrna.1498] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 12/15/2022]
Abstract
The crucial participation of cellular RNA‐binding proteins (RBPs) in virtually all steps of virus infection has been known for decades. However, most of the studies characterizing this phenomenon have focused on well‐established RBPs harboring classical RNA‐binding domains (RBDs). Recent proteome‐wide approaches have greatly expanded the census of RBPs, discovering hundreds of proteins that interact with RNA through unconventional RBDs. These domains include protein–protein interaction platforms, enzymatic cores, and intrinsically disordered regions. Here, we compared the experimentally determined census of RBPs to gene ontology terms and literature, finding that 472 proteins have previous links with viruses. We discuss what these proteins are and what their roles in infection might be. We also review some of the pioneering examples of unorthodox RBPs whose RNA‐binding activity has been shown to be critical for virus infection. Finally, we highlight the potential of these proteins for host‐based therapies against viruses. This article is categorized under:
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
Collapse
Affiliation(s)
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | |
Collapse
|
197
|
Millership SJ, Da Silva Xavier G, Choudhury AI, Bertazzo S, Chabosseau P, Pedroni SM, Irvine EE, Montoya A, Faull P, Taylor WR, Kerr-Conte J, Pattou F, Ferrer J, Christian M, John RM, Latreille M, Liu M, Rutter GA, Scott J, Withers DJ. Neuronatin regulates pancreatic β cell insulin content and secretion. J Clin Invest 2018; 128:3369-3381. [PMID: 29864031 PMCID: PMC6063487 DOI: 10.1172/jci120115] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/17/2018] [Indexed: 02/06/2023] Open
Abstract
Neuronatin (Nnat) is an imprinted gene implicated in human obesity and widely expressed in neuroendocrine and metabolic tissues in a hormone- and nutrient-sensitive manner. However, its molecular and cellular functions and precise role in organismal physiology remain only partly defined. Here we demonstrate that mice lacking Nnat globally or specifically in β cells display impaired glucose-stimulated insulin secretion leading to defective glucose handling under conditions of nutrient excess. In contrast, we report no evidence for any feeding or body weight phenotypes in global Nnat-null mice. At the molecular level neuronatin augments insulin signal peptide cleavage by binding to the signal peptidase complex and facilitates translocation of the nascent preprohormone. Loss of neuronatin expression in β cells therefore reduces insulin content and blunts glucose-stimulated insulin secretion. Nnat expression, in turn, is glucose-regulated. This mechanism therefore represents a novel site of nutrient-sensitive control of β cell function and whole-animal glucose homeostasis. These data also suggest a potential wider role for Nnat in the regulation of metabolism through the modulation of peptide processing events.
Collapse
Affiliation(s)
- Steven J. Millership
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Gabriela Da Silva Xavier
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | | | - Sergio Bertazzo
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Pauline Chabosseau
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Silvia M.A. Pedroni
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Elaine E. Irvine
- MRC London Institute of Medical Sciences, London, United Kingdom
| | - Alex Montoya
- MRC London Institute of Medical Sciences, London, United Kingdom
| | - Peter Faull
- MRC London Institute of Medical Sciences, London, United Kingdom
| | - William R. Taylor
- Computational Cell and Molecular Biology Laboratory, Francis Crick Institute, London, United Kingdom
| | - Julie Kerr-Conte
- European Genomic Institute for Diabetes, UMR 1190 Translational Research for Diabetes, INSERM, CHU Lille, University of Lille, Lille, France
| | - Francois Pattou
- European Genomic Institute for Diabetes, UMR 1190 Translational Research for Diabetes, INSERM, CHU Lille, University of Lille, Lille, France
| | - Jorge Ferrer
- Beta Cell Genome Regulation Laboratory, Department of Medicine, Imperial College London, London, United Kingdom
| | - Mark Christian
- Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Rosalind M. John
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | | | - Ming Liu
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - James Scott
- National Heart and Lung Institute, Department of Medicine, Imperial College London, London, United Kingdom
| | - Dominic J. Withers
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| |
Collapse
|
198
|
Aktepe TE, Mackenzie JM. Shaping the flavivirus replication complex: It is curvaceous! Cell Microbiol 2018; 20:e12884. [PMID: 29933527 PMCID: PMC7162344 DOI: 10.1111/cmi.12884] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/06/2018] [Accepted: 06/14/2018] [Indexed: 12/21/2022]
Abstract
Flavivirus replication is intimately involved with remodelled membrane organelles that are compartmentalised for different functions during their life cycle. Recent advances in lipid analyses and gene depletion have identified a number of host components that enable efficient virus replication in infected cells. Here, we describe the current understanding on the role and contribution of host lipids and membrane bending proteins to flavivirus replication, with a particular focus on the components that bend and shape the membrane bilayer to induce the flavivirus-induced organelles characteristic of infection.
Collapse
Affiliation(s)
- Turgut E. Aktepe
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and ImmunityUniversity of MelbourneMelbourneVICAustralia
| | - Jason M. Mackenzie
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and ImmunityUniversity of MelbourneMelbourneVICAustralia
| |
Collapse
|
199
|
Fujiki J, Nobori H, Sato A, Sasaki M, Carr M, Hall WW, Orba Y, Sawa H. Single Amino Acid Mutation in Dengue Virus NS4B Protein Has Opposing Effects on Viral Proliferation in Mammalian and Mosquito Cells. Jpn J Infect Dis 2018; 71:448-454. [PMID: 30068888 DOI: 10.7883/yoken.jjid.2018.107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Dengue virus (DENV) has a considerable impact on the global health and is known to cause morbidity and mortality every year. By passaging DENV2 in baby hamster kidney (BHK)-21 cells, we isolated a mutant clone of DENV2 that shows rapid cytopathic effects in BHK-21 cells as compared with that showed by the parent strain. To investigate the relationship between amino acid mutations and proliferation activity of the isolated DENV2 clone, we performed full genome sequencing and identified 3 amino acid mutations in the coding region, the envelope T120K, NS4A M85T, and NS4B G124A. Genetically modified recombinant DENV2 (rDENV2) carrying the NS4A M85T and NS4B G124A mutations produced higher titers of progeny virus in BHK-21, Vero, and Huh-7 cells than in the wild-type (WT) rDENV2. rDENV2 with mutations at NS4A M85T and NS4B G124A failed to produce any plaques in C6/36 mosquito cell lines. Furthermore, rDENV2 possessing only the NS4B G124A mutation showed no plaque production in C6/36 cells but had higher viral titers in Vero and Huh-7 cells than the WT rDENV2 had. Our results clearly showed that the DENV2 NS4B G124A mutation has opposing effects on the virus proliferation in mosquito and certain mammalian cell lines.
Collapse
Affiliation(s)
- Jumpei Fujiki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University
| | - Haruaki Nobori
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University.,Drug Discovery & Disease Research Laboratory, Shionogi & Co., Ltd
| | - Akihiko Sato
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University.,Drug Discovery & Disease Research Laboratory, Shionogi & Co., Ltd
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University
| | - Michael Carr
- Global Station for Zoonosis Control, Global Institute for Collaborative Research and Education (GI-CoRE), Hokkaido University.,National Virus Reference Laboratory, School of Medicine, University College Dublin
| | - William Walmsley Hall
- Global Station for Zoonosis Control, Global Institute for Collaborative Research and Education (GI-CoRE), Hokkaido University.,National Virus Reference Laboratory, School of Medicine, University College Dublin.,Global Virus Network.,Centre for Research in Infectious Diseases, School of Medicine, University College Dublin
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University.,Global Station for Zoonosis Control, Global Institute for Collaborative Research and Education (GI-CoRE), Hokkaido University.,Global Virus Network
| |
Collapse
|
200
|
Coyaud E, Ranadheera C, Cheng D, Gonçalves J, Dyakov BJA, Laurent EMN, St-Germain J, Pelletier L, Gingras AC, Brumell JH, Kim PK, Safronetz D, Raught B. Global Interactomics Uncovers Extensive Organellar Targeting by Zika Virus. Mol Cell Proteomics 2018; 17:2242-2255. [PMID: 30037810 DOI: 10.1074/mcp.tir118.000800] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/06/2018] [Indexed: 11/06/2022] Open
Abstract
Zika virus (ZIKV) is a membrane enveloped Flavivirus with a positive strand RNA genome, transmitted by Aedes mosquitoes. The geographical range of ZIKV has dramatically expanded in recent decades resulting in increasing numbers of infected individuals, and the spike in ZIKV infections has been linked to significant increases in both Guillain-Barré syndrome and microcephaly. Although a large number of host proteins have been physically and/or functionally linked to other Flaviviruses, very little is known about the virus-host protein interactions established by ZIKV. Here we map host cell protein interaction profiles for each of the ten polypeptides encoded in the ZIKV genome, generating a protein topology network comprising 3033 interactions among 1224 unique human polypeptides. The interactome is enriched in proteins with roles in polypeptide processing and quality control, vesicle trafficking, RNA processing and lipid metabolism. >60% of the network components have been previously implicated in other types of viral infections; the remaining interactors comprise hundreds of new putative ZIKV functional partners. Mining this rich data set, we highlight several examples of how ZIKV may usurp or disrupt the function of host cell organelles, and uncover an important role for peroxisomes in ZIKV infection.
Collapse
Affiliation(s)
- Etienne Coyaud
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Charlene Ranadheera
- §Public Health Agency of Canada, Zoonotic Diseases and Special Pathogens Program, Winnipeg, Manitoba, Canada
| | - Derrick Cheng
- ¶Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,‖Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - João Gonçalves
- **Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Boris J A Dyakov
- **Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,‡‡Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Estelle M N Laurent
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jonathan St-Germain
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laurence Pelletier
- **Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,‡‡Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- **Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,‡‡Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John H Brumell
- ¶Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,‡‡Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,§§Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,¶¶Sick Kids IBD Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter K Kim
- ¶Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,‖Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - David Safronetz
- §Public Health Agency of Canada, Zoonotic Diseases and Special Pathogens Program, Winnipeg, Manitoba, Canada
| | - Brian Raught
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; .,‖‖Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| |
Collapse
|