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Elste J, Saini A, Mejia-Alvarez R, Mejía A, Millán-Pacheco C, Swanson-Mungerson M, Tiwari V. Significance of Artificial Intelligence in the Study of Virus-Host Cell Interactions. Biomolecules 2024; 14:911. [PMID: 39199298 PMCID: PMC11352483 DOI: 10.3390/biom14080911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/11/2024] [Accepted: 07/23/2024] [Indexed: 09/01/2024] Open
Abstract
A highly critical event in a virus's life cycle is successfully entering a given host. This process begins when a viral glycoprotein interacts with a target cell receptor, which provides the molecular basis for target virus-host cell interactions for novel drug discovery. Over the years, extensive research has been carried out in the field of virus-host cell interaction, generating a massive number of genetic and molecular data sources. These datasets are an asset for predicting virus-host interactions at the molecular level using machine learning (ML), a subset of artificial intelligence (AI). In this direction, ML tools are now being applied to recognize patterns in these massive datasets to predict critical interactions between virus and host cells at the protein-protein and protein-sugar levels, as well as to perform transcriptional and translational analysis. On the other end, deep learning (DL) algorithms-a subfield of ML-can extract high-level features from very large datasets to recognize the hidden patterns within genomic sequences and images to develop models for rapid drug discovery predictions that address pathogenic viruses displaying heightened affinity for receptor docking and enhanced cell entry. ML and DL are pivotal forces, driving innovation with their ability to perform analysis of enormous datasets in a highly efficient, cost-effective, accurate, and high-throughput manner. This review focuses on the complexity of virus-host cell interactions at the molecular level in light of the current advances of ML and AI in viral pathogenesis to improve new treatments and prevention strategies.
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Affiliation(s)
- James Elste
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (M.S.-M.)
| | - Akash Saini
- Hinsdale Central High School, 5500 S Grant St, Hinsdale, IL 60521, USA;
| | - Rafael Mejia-Alvarez
- Department of Physiology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA;
| | - Armando Mejía
- Departamento de Biotechnology, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de Mexico 09340, Mexico;
| | - Cesar Millán-Pacheco
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad No. 1001, Col Chamilpa, Cuernavaca 62209, Mexico;
| | - Michelle Swanson-Mungerson
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (M.S.-M.)
| | - Vaibhav Tiwari
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (M.S.-M.)
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Raju S, Adams LJ, Diamond MS. The many ways in which alphaviruses bind to cells. Trends Immunol 2024; 45:85-93. [PMID: 38135598 PMCID: PMC10997154 DOI: 10.1016/j.it.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/25/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023]
Abstract
Only a subset of viruses can productively infect many different host species. Some arthropod-transmitted viruses, such as alphaviruses, can infect invertebrate and vertebrate species including insects, reptiles, birds, and mammals. This broad tropism may be explained by their ability to engage receptors that are conserved across vertebrate and invertebrate classes. Through several genome-wide loss-of-function screens, new alphavirus receptors have been identified, some of which bind to multiple related viruses in different antigenic complexes. Structural analysis has revealed that distinct sites on the alphavirus glycoprotein can mediate receptor binding, which opposes the idea that a single receptor-binding site mediates viral entry. Here, we discuss how different paradigms of receptor engagement on cells might explain the promiscuity of alphaviruses for multiple hosts.
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Affiliation(s)
- Saravanan Raju
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lucas J Adams
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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Zimmerman O, Holmes AC, Kafai NM, Adams LJ, Diamond MS. Entry receptors - the gateway to alphavirus infection. J Clin Invest 2023; 133:e165307. [PMID: 36647825 PMCID: PMC9843064 DOI: 10.1172/jci165307] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Alphaviruses are enveloped, insect-transmitted, positive-sense RNA viruses that infect humans and other animals and cause a range of clinical manifestations, including arthritis, musculoskeletal disease, meningitis, encephalitis, and death. Over the past four years, aided by CRISPR/Cas9-based genetic screening approaches, intensive research efforts have focused on identifying entry receptors for alphaviruses to better understand the basis for cellular and species tropism. Herein, we review approaches to alphavirus receptor identification and how these were used for discovery. The identification of new receptors advances our understanding of viral pathogenesis, tropism, and evolution and is expected to contribute to the development of novel strategies for prevention and treatment of alphavirus infection.
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Affiliation(s)
| | | | | | | | - Michael S. Diamond
- Department of Medicine
- Department of Pathology and Immunology
- Department of Molecular Microbiology, and
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, Missouri, USA
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4
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Yuan F, Zheng A. Replicating-Competent VSV-Vectored Pseudotyped Viruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1407:329-348. [PMID: 36920706 DOI: 10.1007/978-981-99-0113-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Vesicular stomatitis virus (VSV) is prototype virus in the family of Rhabdoviridae. Reverse genetic platform has enabled the genetic manipulation of VSV as a powerful live viral vector. Replicating-competent VSV is constructed by replacing the original VSV glycoprotein gene with heterologous envelope genes. The resulting recombinant viruses are able to replicate in permissive cells and incorporate the foreign envelope proteins on the surface of the viral particle without changing the bullet-shape morphology. Correspondingly, the cell tropism of replicating-competent VSV is determined by the foreign envelope proteins. Replicating-competent VSVs have been successfully used for selecting critical viral receptors or host factors, screening mutants that escape therapeutic antibodies, and developing VSV-based live viral vaccines.
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Affiliation(s)
- Fei Yuan
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Aihua Zheng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
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5
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Gao SS, Shi R, Sun J, Tang Y, Zheng Z, Li JF, Li H, Zhang J, Leng Q, Xu J, Chen X, Zhao J, Sy MS, Feng L, Li C. GPI-anchored ligand-BioID2-tagging system identifies Galectin-1 mediating Zika virus entry. iScience 2022; 25:105481. [PMID: 36404916 PMCID: PMC9668739 DOI: 10.1016/j.isci.2022.105481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/30/2022] [Accepted: 10/28/2022] [Indexed: 11/15/2022] Open
Abstract
Identification of host factors facilitating pathogen entry is critical for preventing infectious diseases. Here, we report a tagging system consisting of a viral receptor-binding protein (RBP) linked to BioID2, which is expressed on the cell surface via a GPI anchor. Using VSV or Zika virus (ZIKV) RBP, the system (BioID2- RBP(V)-GPI; BioID2-RBP(Z)-GPI) faithfully identifies LDLR and AXL, the receptors of VSV and ZIKV, respectively. Being GPI-anchored is essential for the probe to function properly. Furthermore, BioID2-RBP(Z)-GPI expressed in human neuronal progenitor cells identifies galectin-1 on cell surface pivotal for ZIKV entry. This conclusion is further supported by antibody blocking and galectin-1 silencing in A549 and mouse neural cells. Importantly, Lgals1−/− mice are significantly more resistant to ZIKV infection than Lgals1+/+ littermates are, having significantly lower virus titers and fewer pathologies in various organs. This tagging system may have broad applications for identifying protein-protein interactions on the cell surface. A tagging system for identifying ligand-receptor interactions is developed Receptor binding domain determines the specificity of the system Being GPI-anchored is pivotal for the tagging system to function properly Galectin-1 is identified as an entry factor essential for ZIKV infection
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Abdulhasan M, Ruden X, Rappolee B, Dutta S, Gurdziel K, Ruden DM, Awonuga AO, Korzeniewski SJ, Puscheck EE, Rappolee DA. Stress Decreases Host Viral Resistance and Increases Covid Susceptibility in Embryonic Stem Cells. Stem Cell Rev Rep 2021; 17:2164-2177. [PMID: 34155611 PMCID: PMC8216586 DOI: 10.1007/s12015-021-10188-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 12/13/2022]
Abstract
Stress-induced changes in viral receptor and susceptibility gene expression were measured in embryonic stem cells (ESC) and differentiated progeny. Rex1 promoter-Red Fluorescence Protein reporter ESC were tested by RNAseq after 72hr exposures to control stress hyperosmotic sorbitol under stemness culture (NS) to quantify stress-forced differentiation (SFD) transcriptomic programs. Control ESC cultured with stemness factor removal produced normal differentiation (ND). Bulk RNAseq transcriptomic analysis showed significant upregulation of two genes involved in Covid-19 cell uptake, Vimentin (VIM) and Transmembrane Serine Protease 2 (TMPRSS2). SFD increased the hepatitis A virus receptor (Havcr1) and the transplacental Herpes simplex 1 (HSV1) virus receptor (Pvrl1) compared with ESC undergoing ND. Several other coronavirus receptors, Glutamyl Aminopeptidase (ENPEP) and Dipeptidyl Peptidase 4 (DPP4) were upregulated significantly in SFD>ND. Although stressed ESC are more susceptible to infection due to increased expression of viral receptors and decreased resistance, the necessary Covid-19 receptor, angiotensin converting enzyme (ACE)2, was not expressed in our experiments. TMPRSS2, ENPEP, and DPP4 mediate Coronavirus uptake, but are also markers of extra-embryonic endoderm (XEN), which arise from ESC undergoing ND or SFD. Mouse and human ESCs differentiated to XEN increase TMPRSS2 and other Covid-19 uptake-mediating gene expression, but only some lines express ACE2. Covid-19 susceptibility appears to be genotype-specific and not ubiquitous. Of the 30 gene ontology (GO) groups for viral susceptibility, 15 underwent significant stress-forced changes. Of these, 4 GO groups mediated negative viral regulation and most genes in these increase in ND and decrease with SFD, thus suggesting that stress increases ESC viral susceptibility. Taken together, the data suggest that a control hyperosmotic stress can increase Covid-19 susceptibility and decrease viral host resistance in mouse ESC. However, this limited pilot study should be followed with studies in human ESC, tests of environmental, hormonal, and pharmaceutical stressors and direct tests for infection of stressed, cultured ESC and embryos by Covid-19.
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Affiliation(s)
- Mohammed Abdulhasan
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
- Reproductive Stress 3M Inc, Grosse Pointe Farms, MI, 48236, USA
| | - Ximena Ruden
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
| | | | - Sudipta Dutta
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
- Reproductive Endocrinology and Cell Signaling LaboratoryDepartment of Integrative BiosciencesCollege of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, USA
| | - Katherine Gurdziel
- Genome Sciences Center, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Douglas M Ruden
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
- Institutes for Environmental Health Science, Wayne State University School of Medicine, Detroit, 48202, USA
| | - Awoniyi O Awonuga
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
| | - Steve J Korzeniewski
- Institutes for Environmental Health Science, Wayne State University School of Medicine, Detroit, 48202, USA
| | - Elizabeth E Puscheck
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
- Reproductive Stress 3M Inc, Grosse Pointe Farms, MI, 48236, USA
- Invia Fertility Clinics, Hoffman Estates, Illinois, 60169, USA
| | - Daniel A Rappolee
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA.
- Reproductive Stress 3M Inc, Grosse Pointe Farms, MI, 48236, USA.
- Institutes for Environmental Health Science, Wayne State University School of Medicine, Detroit, 48202, USA.
- Program for Reproductive Sciences and Department of Physiology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
- Department of Biology, University of Windsor, Windsor, ON, N9B 3P4, Canada.
- CS Mott Center for Human Growth and Development, Wayne State University School of Medicine, 275 East Hancock, Detroit, MI, 48201, USA.
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Kirby EN, Shue B, Thomas PQ, Beard MR. CRISPR Tackles Emerging Viral Pathogens. Viruses 2021; 13:2157. [PMID: 34834963 PMCID: PMC8624524 DOI: 10.3390/v13112157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 12/17/2022] Open
Abstract
Understanding the dynamic relationship between viral pathogens and cellular host factors is critical to furthering our knowledge of viral replication, disease mechanisms and development of anti-viral therapeutics. CRISPR genome editing technology has enhanced this understanding, by allowing identification of pro-viral and anti-viral cellular host factors for a wide range of viruses, most recently the cause of the COVID-19 pandemic, SARS-CoV-2. This review will discuss how CRISPR knockout and CRISPR activation genome-wide screening methods are a robust tool to investigate the viral life cycle and how other class 2 CRISPR systems are being repurposed for diagnostics.
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Affiliation(s)
- Emily N. Kirby
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia; (E.N.K.); (B.S.)
| | - Byron Shue
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia; (E.N.K.); (B.S.)
| | - Paul Q. Thomas
- Adelaide Medical School, The University of Adelaide, Adelaide 5000, Australia;
- Robinson Research Institute, The University of Adelaide, Adelaide 5006, Australia
- Genome Editing Program, South Australian Health & Medical Research Institute, North Terrace, Adelaide 5000, Australia
| | - Michael R. Beard
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia; (E.N.K.); (B.S.)
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8
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Hulswit RJG, Paesen GC, Bowden TA, Shi X. Recent Advances in Bunyavirus Glycoprotein Research: Precursor Processing, Receptor Binding and Structure. Viruses 2021; 13:353. [PMID: 33672327 PMCID: PMC7926653 DOI: 10.3390/v13020353] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 01/04/2023] Open
Abstract
The Bunyavirales order accommodates related viruses (bunyaviruses) with segmented, linear, single-stranded, negative- or ambi-sense RNA genomes. Their glycoproteins form capsomeric projections or spikes on the virion surface and play a crucial role in virus entry, assembly, morphogenesis. Bunyavirus glycoproteins are encoded by a single RNA segment as a polyprotein precursor that is co- and post-translationally cleaved by host cell enzymes to yield two mature glycoproteins, Gn and Gc (or GP1 and GP2 in arenaviruses). These glycoproteins undergo extensive N-linked glycosylation and despite their cleavage, remain associated to the virion to form an integral transmembrane glycoprotein complex. This review summarizes recent advances in our understanding of the molecular biology of bunyavirus glycoproteins, including their processing, structure, and known interactions with host factors that facilitate cell entry.
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Affiliation(s)
- Ruben J. G. Hulswit
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (R.J.G.H.); (G.C.P.)
| | - Guido C. Paesen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (R.J.G.H.); (G.C.P.)
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (R.J.G.H.); (G.C.P.)
| | - Xiaohong Shi
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G61 1QH, UK
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Peters CE, Carette JE. Return of the Neurotropic Enteroviruses: Co-Opting Cellular Pathways for Infection. Viruses 2021; 13:v13020166. [PMID: 33499355 PMCID: PMC7911124 DOI: 10.3390/v13020166] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 02/06/2023] Open
Abstract
Enteroviruses are among the most common human infectious agents. While infections are often mild, the severe neuropathogenesis associated with recent outbreaks of emerging non-polio enteroviruses, such as EV-A71 and EV-D68, highlights their continuing threat to public health. In recent years, our understanding of how non-polio enteroviruses co-opt cellular pathways has greatly increased, revealing intricate host-virus relationships. In this review, we focus on newly identified mechanisms by which enteroviruses hijack the cellular machinery to promote their replication and spread, and address their potential for the development of host-directed therapeutics. Specifically, we discuss newly identified cellular receptors and their contribution to neurotropism and spread, host factors required for viral entry and replication, and recent insights into lipid acquisition and replication organelle biogenesis. The comprehensive knowledge of common cellular pathways required by enteroviruses could expose vulnerabilities amenable for host-directed therapeutics against a broad spectrum of enteroviruses. Since this will likely include newly arising strains, it will better prepare us for future epidemics. Moreover, identifying host proteins specific to neurovirulent strains may allow us to better understand factors contributing to the neurotropism of these viruses.
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E3 ubiquitin ligase Mindbomb 1 facilitates nuclear delivery of adenovirus genomes. Proc Natl Acad Sci U S A 2020; 118:2015794118. [PMID: 33443154 DOI: 10.1073/pnas.2015794118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The journey from plasma membrane to nuclear pore is a critical step in the lifecycle of DNA viruses, many of which must successfully deposit their genomes into the nucleus for replication. Viral capsids navigate this vast distance through the coordinated hijacking of a number of cellular host factors, many of which remain unknown. We performed a gene-trap screen in haploid cells to identify host factors for adenovirus (AdV), a DNA virus that can cause severe respiratory illness in immune-compromised individuals. This work identified Mindbomb 1 (MIB1), an E3 ubiquitin ligase involved in neurodevelopment, as critical for AdV infectivity. In the absence of MIB1, we observed that viral capsids successfully traffic to the proximity of the nucleus but ultimately fail to deposit their genomes within. The capacity of MIB1 to promote AdV infection was dependent on its ubiquitination activity, suggesting that MIB1 may mediate proteasomal degradation of one or more negative regulators of AdV infection. Employing complementary proteomic approaches to characterize proteins proximal to MIB1 upon AdV infection and differentially ubiquitinated in the presence or absence of MIB1, we observed an intersection between MIB1 and ribonucleoproteins (RNPs) largely unexplored in mammalian cells. This work uncovers yet another way that viruses utilize host cell machinery for their own replication, highlighting a potential target for therapeutic interventions that counter AdV infection.
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Zengel J, Carette JE. Structural and cellular biology of adeno-associated virus attachment and entry. Adv Virus Res 2020; 106:39-84. [PMID: 32327148 DOI: 10.1016/bs.aivir.2020.01.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Adeno-associated virus (AAV) is a nonenveloped, ssDNA virus in the parvovirus family, which has become one of the leading candidate vectors for human gene therapy. AAV has been studied extensively to identify host cellular factors involved in infection, as well as to identify capsid variants that confer clinically favorable transduction profiles ex vivo and in vivo. Recent advances in technology have allowed for direct genetic approaches to be used to more comprehensively characterize host factors required for AAV infection and allowed for identification of a critical multi-serotype receptor, adeno-associated virus receptor (AAVR). In this chapter, we will discuss the interactions of AAV with its glycan and proteinaceous receptors and describe the host and viral components involved in AAV entry, which requires cellular attachment, endocytosis, trafficking to the trans-Golgi network and nuclear import. AAV serves as a paradigm for entry of nonenveloped viruses. Furthermore, we will discuss the potential of utilizing our increased understanding of virus-host interactions during AAV entry to develop better AAV-based therapeutics, with a focus on host factors and capsid interactions involved in in vivo tropism.
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12
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Barrass SV, Butcher SJ. Advances in high-throughput methods for the identification of virus receptors. Med Microbiol Immunol 2019; 209:309-323. [PMID: 31865406 PMCID: PMC7248041 DOI: 10.1007/s00430-019-00653-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/02/2019] [Indexed: 12/26/2022]
Abstract
Viruses have evolved many mechanisms to invade host cells and establish successful infections. The interaction between viral attachment proteins and host cell receptors is the first and decisive step in establishing such infections, initiating virus entry into the host cells. Therefore, the identification of host receptors is fundamental in understanding pathogenesis and tissue tropism. Furthermore, receptor identification can inform the development of antivirals, vaccines, and diagnostic technologies, which have a substantial impact on human health. Nevertheless, due to the complex nature of virus entry, the redundancy in receptor usage, and the limitations in current identification methods, many host receptors remain elusive. Recent advances in targeted gene perturbation, high-throughput screening, and mass spectrometry have facilitated the discovery of virus receptors in recent years. In this review, we compare the current methods used within the field to identify virus receptors, focussing on genomic- and interactome-based approaches.
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Affiliation(s)
- Sarah V Barrass
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme and Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
| | - Sarah J Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme and Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
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13
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Protocadherin-1 is essential for cell entry by New World hantaviruses. Nature 2018; 563:559-563. [PMID: 30464266 DOI: 10.1038/s41586-018-0702-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 09/20/2018] [Indexed: 01/26/2023]
Abstract
The zoonotic transmission of hantaviruses from their rodent hosts to humans in North and South America is associated with a severe and frequently fatal respiratory disease, hantavirus pulmonary syndrome (HPS)1,2. No specific antiviral treatments for HPS are available, and no molecular determinants of in vivo susceptibility to hantavirus infection and HPS are known. Here we identify the human asthma-associated gene protocadherin-1 (PCDH1)3-6 as an essential determinant of entry and infection in pulmonary endothelial cells by two hantaviruses that cause HPS, Andes virus (ANDV) and Sin Nombre virus (SNV). In vitro, we show that the surface glycoproteins of ANDV and SNV directly recognize the outermost extracellular repeat domain of PCDH1-a member of the cadherin superfamily7,8-to exploit PCDH1 for entry. In vivo, genetic ablation of PCDH1 renders Syrian golden hamsters highly resistant to a usually lethal ANDV challenge. Targeting PCDH1 could provide strategies to reduce infection and disease caused by New World hantaviruses.
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14
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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.
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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.
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15
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Lasswitz L, Chandra N, Arnberg N, Gerold G. Glycomics and Proteomics Approaches to Investigate Early Adenovirus-Host Cell Interactions. J Mol Biol 2018; 430:1863-1882. [PMID: 29746851 PMCID: PMC7094377 DOI: 10.1016/j.jmb.2018.04.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/24/2018] [Accepted: 04/30/2018] [Indexed: 12/14/2022]
Abstract
Adenoviruses as most viruses rely on glycan and protein interactions to attach to and enter susceptible host cells. The Adenoviridae family comprises more than 80 human types and they differ in their attachment factor and receptor usage, which likely contributes to the diverse tropism of the different types. In the past years, methods to systematically identify glycan and protein interactions have advanced. In particular sensitivity, speed and coverage of mass spectrometric analyses allow for high-throughput identification of glycans and peptides separated by liquid chromatography. Also, developments in glycan microarray technologies have led to targeted, high-throughput screening and identification of glycan-based receptors. The mapping of cell surface interactions of the diverse adenovirus types has implications for cell, tissue, and species tropism as well as drug development. Here we review known adenovirus interactions with glycan- and protein-based receptors, as well as glycomics and proteomics strategies to identify yet elusive virus receptors and attachment factors. We finally discuss challenges, bottlenecks, and future research directions in the field of non-enveloped virus entry into host cells.
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Affiliation(s)
- Lisa Lasswitz
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
| | - Naresh Chandra
- Department of Clinical Microbiology, Virology, Umeå University, SE-90185 Umeå, Sweden; Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-90185 Umea, Sweden
| | - Niklas Arnberg
- Department of Clinical Microbiology, Virology, Umeå University, SE-90185 Umeå, Sweden; Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-90185 Umea, Sweden.
| | - Gisa Gerold
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, SE-90185 Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, SE-90185 Umea, Sweden.
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16
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Loregger A, Raaben M, Tan J, Scheij S, Moeton M, van den Berg M, Gelberg-Etel H, Stickel E, Roitelman J, Brummelkamp T, Zelcer N. Haploid Mammalian Genetic Screen Identifies UBXD8 as a Key Determinant of HMGCR Degradation and Cholesterol Biosynthesis. Arterioscler Thromb Vasc Biol 2017; 37:2064-2074. [PMID: 28882874 PMCID: PMC5671778 DOI: 10.1161/atvbaha.117.310002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/29/2017] [Indexed: 01/23/2023]
Abstract
Supplemental Digital Content is available in the text. Objective— The cellular demand for cholesterol requires control of its biosynthesis by the mevalonate pathway. Regulation of HMGCR (3-hydroxy-3-methylglutaryl coenzyme A reductase), a rate-limiting enzyme in this pathway and the target of statins, is a key control point herein. Accordingly, HMGCR is subject to negative and positive regulation. In particular, the ability of oxysterols and intermediates of the mevalonate pathway to stimulate its proteasomal degradation is an exquisite example of metabolically controlled feedback regulation. To define the genetic determinants that govern this process, we conducted an unbiased haploid mammalian genetic screen. Approach and Results— We generated human haploid cells with mNeon fused to endogenous HMGCR using CRISPR/Cas9 and used these cells to interrogate regulation of HMGCR abundance in live cells. This resulted in identification of known and new regulators of HMGCR, and among the latter, UBXD8 (ubiquitin regulatory X domain-containing protein 8), a gene that has not been previously implicated in this process. We demonstrate that UBXD8 is an essential determinant of metabolically stimulated degradation of HMGCR and of cholesterol biosynthesis in multiple cell types. Accordingly, UBXD8 ablation leads to aberrant cholesterol synthesis due to loss of feedback control. Mechanistically, we show that UBXD8 is necessary for sterol-stimulated dislocation of ubiquitylated HMGCR from the endoplasmic reticulum membrane en route to proteasomal degradation, a function dependent on its UBX domain. Conclusions— We establish UBXD8 as a previously unrecognized determinant that couples flux across the mevalonate pathway to control of cholesterol synthesis and demonstrate the feasibility of applying mammalian haploid genetics to study metabolic traits.
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Affiliation(s)
- Anke Loregger
- From the Department of Medical Biochemistry, Academic Medical Center of the University of Amsterdam, The Netherlands (A.L., J.T., S.S., M.M., M.v.d.B., N.Z.); Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam (M.R., E.S., T.B.); CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna (T.B.); Cancer GenomiCs.nl, Amsterdam, The Netherlands (T.B.); Bert W. Strassburger Lipid Center, Sheba Medical Center, Tel Hashomer, Israel (H.G.-E., J.R.); and Department of Human Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel (H.G.-E., J.R.)
| | - Matthijs Raaben
- From the Department of Medical Biochemistry, Academic Medical Center of the University of Amsterdam, The Netherlands (A.L., J.T., S.S., M.M., M.v.d.B., N.Z.); Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam (M.R., E.S., T.B.); CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna (T.B.); Cancer GenomiCs.nl, Amsterdam, The Netherlands (T.B.); Bert W. Strassburger Lipid Center, Sheba Medical Center, Tel Hashomer, Israel (H.G.-E., J.R.); and Department of Human Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel (H.G.-E., J.R.)
| | - Josephine Tan
- From the Department of Medical Biochemistry, Academic Medical Center of the University of Amsterdam, The Netherlands (A.L., J.T., S.S., M.M., M.v.d.B., N.Z.); Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam (M.R., E.S., T.B.); CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna (T.B.); Cancer GenomiCs.nl, Amsterdam, The Netherlands (T.B.); Bert W. Strassburger Lipid Center, Sheba Medical Center, Tel Hashomer, Israel (H.G.-E., J.R.); and Department of Human Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel (H.G.-E., J.R.)
| | - Saskia Scheij
- From the Department of Medical Biochemistry, Academic Medical Center of the University of Amsterdam, The Netherlands (A.L., J.T., S.S., M.M., M.v.d.B., N.Z.); Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam (M.R., E.S., T.B.); CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna (T.B.); Cancer GenomiCs.nl, Amsterdam, The Netherlands (T.B.); Bert W. Strassburger Lipid Center, Sheba Medical Center, Tel Hashomer, Israel (H.G.-E., J.R.); and Department of Human Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel (H.G.-E., J.R.)
| | - Martina Moeton
- From the Department of Medical Biochemistry, Academic Medical Center of the University of Amsterdam, The Netherlands (A.L., J.T., S.S., M.M., M.v.d.B., N.Z.); Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam (M.R., E.S., T.B.); CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna (T.B.); Cancer GenomiCs.nl, Amsterdam, The Netherlands (T.B.); Bert W. Strassburger Lipid Center, Sheba Medical Center, Tel Hashomer, Israel (H.G.-E., J.R.); and Department of Human Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel (H.G.-E., J.R.)
| | - Marlene van den Berg
- From the Department of Medical Biochemistry, Academic Medical Center of the University of Amsterdam, The Netherlands (A.L., J.T., S.S., M.M., M.v.d.B., N.Z.); Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam (M.R., E.S., T.B.); CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna (T.B.); Cancer GenomiCs.nl, Amsterdam, The Netherlands (T.B.); Bert W. Strassburger Lipid Center, Sheba Medical Center, Tel Hashomer, Israel (H.G.-E., J.R.); and Department of Human Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel (H.G.-E., J.R.)
| | - Hila Gelberg-Etel
- From the Department of Medical Biochemistry, Academic Medical Center of the University of Amsterdam, The Netherlands (A.L., J.T., S.S., M.M., M.v.d.B., N.Z.); Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam (M.R., E.S., T.B.); CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna (T.B.); Cancer GenomiCs.nl, Amsterdam, The Netherlands (T.B.); Bert W. Strassburger Lipid Center, Sheba Medical Center, Tel Hashomer, Israel (H.G.-E., J.R.); and Department of Human Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel (H.G.-E., J.R.)
| | - Elmer Stickel
- From the Department of Medical Biochemistry, Academic Medical Center of the University of Amsterdam, The Netherlands (A.L., J.T., S.S., M.M., M.v.d.B., N.Z.); Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam (M.R., E.S., T.B.); CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna (T.B.); Cancer GenomiCs.nl, Amsterdam, The Netherlands (T.B.); Bert W. Strassburger Lipid Center, Sheba Medical Center, Tel Hashomer, Israel (H.G.-E., J.R.); and Department of Human Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel (H.G.-E., J.R.)
| | - Joseph Roitelman
- From the Department of Medical Biochemistry, Academic Medical Center of the University of Amsterdam, The Netherlands (A.L., J.T., S.S., M.M., M.v.d.B., N.Z.); Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam (M.R., E.S., T.B.); CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna (T.B.); Cancer GenomiCs.nl, Amsterdam, The Netherlands (T.B.); Bert W. Strassburger Lipid Center, Sheba Medical Center, Tel Hashomer, Israel (H.G.-E., J.R.); and Department of Human Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel (H.G.-E., J.R.)
| | - Thijn Brummelkamp
- From the Department of Medical Biochemistry, Academic Medical Center of the University of Amsterdam, The Netherlands (A.L., J.T., S.S., M.M., M.v.d.B., N.Z.); Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam (M.R., E.S., T.B.); CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna (T.B.); Cancer GenomiCs.nl, Amsterdam, The Netherlands (T.B.); Bert W. Strassburger Lipid Center, Sheba Medical Center, Tel Hashomer, Israel (H.G.-E., J.R.); and Department of Human Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel (H.G.-E., J.R.)
| | - Noam Zelcer
- From the Department of Medical Biochemistry, Academic Medical Center of the University of Amsterdam, The Netherlands (A.L., J.T., S.S., M.M., M.v.d.B., N.Z.); Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam (M.R., E.S., T.B.); CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna (T.B.); Cancer GenomiCs.nl, Amsterdam, The Netherlands (T.B.); Bert W. Strassburger Lipid Center, Sheba Medical Center, Tel Hashomer, Israel (H.G.-E., J.R.); and Department of Human Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel (H.G.-E., J.R.).
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17
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Pillay S, Carette JE. Host determinants of adeno-associated viral vector entry. Curr Opin Virol 2017; 24:124-131. [PMID: 28672171 DOI: 10.1016/j.coviro.2017.06.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 05/28/2017] [Accepted: 06/09/2017] [Indexed: 12/18/2022]
Abstract
Viral vectors based on adeno-associated virus (AAV) are leading candidates for therapeutic gene delivery. Understanding rate-limiting steps in the entry of AAV vectors may be used in a rational approach to improve efficiency and specificity of transduction. This review describes our current understanding of AAV entry, a key step during infection. We discuss the identity and functions of AAV receptors and attachment factors, including the recently discovered multi-serotype receptor AAVR. We further provide an overview of other host factors that act during the trafficking stage of AAV vector transduction. In particular, we focus on cellular protein complexes associated with retrograde transport from endosomes to the trans-Golgi network. The novel insights in AAV-host interactions facilitated by technological advances in genetic screening approaches provide a greater depth in our understanding how AAV vectors exploit host factors to deliver its genetic cargo to the nucleus.
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Affiliation(s)
- Sirika Pillay
- Stanford University, Department of Microbiology and Immunology, Stanford, CA 94305, USA
| | - Jan E Carette
- Stanford University, Department of Microbiology and Immunology, Stanford, CA 94305, USA.
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18
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Puschnik AS, Majzoub K, Ooi YS, Carette JE. A CRISPR toolbox to study virus-host interactions. Nat Rev Microbiol 2017; 15:351-364. [PMID: 28420884 PMCID: PMC5800792 DOI: 10.1038/nrmicro.2017.29] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Viruses are obligate intracellular pathogens that depend on host cellular components for replication. Genetic screens are an unbiased and comprehensive method to uncover host cellular components that are critical for the infection with viruses. Loss-of-function screens result in the genome-wide disruption of gene expression, whereas gain-of-function screens rely on large-scale overexpression of host genes. Genetic knockout screens can be conducted using haploid insertional mutagenesis or the CRISPR–Cas system. Genetic screens using the CRISPR–Cas system have provided crucial insights in the host determinants of infections with important human pathogens such as dengue virus, West Nile virus, Zika virus and hepatitis C virus. CRISPR–Cas-based techniques additionally provide ways to generate both in vitro and in vivo models to study viral pathogenesis, to manipulate viral genomes, to eradicate viral disease vectors using gene drive systems and to advance the development of antiviral therapeutics.
In this Review, Puschnik and colleagues discuss the technical aspects of using CRISPR–Cas technology in genome-scale knockout screens to study virus–host interactions, and they compare these screens with alternative genetic screening technologies. Viruses depend on their hosts to complete their replication cycles; they exploit cellular receptors for entry and hijack cellular functions to replicate their genome, assemble progeny virions and spread. Recently, genome-scale CRISPR–Cas screens have been used to identify host factors that are required for virus replication, including the replication of clinically relevant viruses such as Zika virus, West Nile virus, dengue virus and hepatitis C virus. In this Review, we discuss the technical aspects of genome-scale knockout screens using CRISPR–Cas technology, and we compare these screens with alternative genetic screening technologies. The relative ease of use and reproducibility of CRISPR–Cas make it a powerful tool for probing virus–host interactions and for identifying new antiviral targets.
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Affiliation(s)
- Andreas S Puschnik
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
| | - Karim Majzoub
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
| | - Yaw Shin Ooi
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
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19
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Affiliation(s)
| | - R. Jude Samulski
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
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