1
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Wong CH, Wingett SW, Qian C, Hunter MR, Taliaferro JM, Ross-Thriepland D, Bullock SL. Genome-scale requirements for dynein-based transport revealed by a high-content arrayed CRISPR screen. J Cell Biol 2024; 223:e202306048. [PMID: 38448164 PMCID: PMC10916854 DOI: 10.1083/jcb.202306048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 01/10/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
The microtubule motor dynein plays a key role in cellular organization. However, little is known about how dynein's biosynthesis, assembly, and functional diversity are orchestrated. To address this issue, we have conducted an arrayed CRISPR loss-of-function screen in human cells using the distribution of dynein-tethered peroxisomes and early endosomes as readouts. From a genome-wide gRNA library, 195 validated hits were recovered and parsed into those impacting multiple dynein cargoes and those whose effects are restricted to a subset of cargoes. Clustering of high-dimensional phenotypic fingerprints revealed co-functional proteins involved in many cellular processes, including several candidate novel regulators of core dynein functions. Further analysis of one of these factors, the RNA-binding protein SUGP1, indicates that it promotes cargo trafficking by sustaining functional expression of the dynein activator LIS1. Our data represent a rich source of new hypotheses for investigating microtubule-based transport, as well as several other aspects of cellular organization captured by our high-content imaging.
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Affiliation(s)
- Chun Hao Wong
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Centre for Genomic Research, Discovery Sciences, AstraZeneca , Cambridge, UK
| | - Steven W Wingett
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Chen Qian
- Quantitative Biology, Discovery Sciences, AstraZeneca , Cambridge, UK
| | - Morag Rose Hunter
- Centre for Genomic Research, Discovery Sciences, AstraZeneca , Cambridge, UK
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Simon L Bullock
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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2
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Hunter MR, Cui L, Porebski BT, Pereira S, Sonzini S, Odunze U, Iyer P, Engkvist O, Lloyd RL, Peel S, Sabirsh A, Ross-Thriepland D, Jones AT, Desai AS. Understanding Intracellular Biology to Improve mRNA Delivery by Lipid Nanoparticles. Small Methods 2023; 7:e2201695. [PMID: 37317010 PMCID: PMC7615154 DOI: 10.1002/smtd.202201695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/06/2023] [Indexed: 06/16/2023]
Abstract
Poor understanding of intracellular delivery and targeting hinders development of nucleic acid-based therapeutics transported by nanoparticles. Utilizing a siRNA-targeting and small molecule profiling approach with advanced imaging and machine learning biological insights is generated into the mechanism of lipid nanoparticle (MC3-LNP) delivery of mRNA. This workflow is termed Advanced Cellular and Endocytic profiling for Intracellular Delivery (ACE-ID). A cell-based imaging assay and perturbation of 178 targets relevant to intracellular trafficking is used to identify corresponding effects on functional mRNA delivery. Targets improving delivery are analyzed by extracting data-rich phenotypic fingerprints from images using advanced image analysis algorithms. Machine learning is used to determine key features correlating with enhanced delivery, identifying fluid-phase endocytosis as a productive cellular entry route. With this new knowledge, MC3-LNP is re-engineered to target macropinocytosis, and this significantly improves mRNA delivery in vitro and in vivo. The ACE-ID approach can be broadly applicable for optimizing nanomedicine-based intracellular delivery systems and has the potential to accelerate the development of delivery systems for nucleic acid-based therapeutics.
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Affiliation(s)
- Morag Rose Hunter
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Cambridge, CB21 6GH, UK
| | - Lili Cui
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Cambridge, CB21 6GH, UK
| | | | - Sara Pereira
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Cambridge, CB21 6GH, UK
| | - Silvia Sonzini
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Cambridge, CB21 6GH, UK
| | - Uchechukwu Odunze
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Cambridge, CB21 6GH, UK
| | - Preeti Iyer
- Molecular AI, Discovery Sciences, R&D, Astrazeneca, Gothenburg, 431 50, Sweden
| | - Ola Engkvist
- Molecular AI, Discovery Sciences, R&D, Astrazeneca, Gothenburg, 431 50, Sweden
| | - Rebecca Louise Lloyd
- Functional Genomics, Discovery Sciences, R&D, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Samantha Peel
- Functional Genomics, Discovery Sciences, R&D, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Alan Sabirsh
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, 431 50, Sweden
| | | | - Arwyn Tomos Jones
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, UK
| | - Arpan Shailesh Desai
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Cambridge, CB21 6GH, UK
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3
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Wong CH, Wingett SW, Qian C, Taliaferro JM, Ross-Thriepland D, Bullock SL. Genome-scale requirements for dynein-based trafficking revealed by a high-content arrayed CRISPR screen. bioRxiv 2023:2023.03.01.530592. [PMID: 36909483 PMCID: PMC10002790 DOI: 10.1101/2023.03.01.530592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The cytoplasmic dynein-1 (dynein) motor plays a key role in cellular organisation by transporting a wide variety of cellular constituents towards the minus ends of microtubules. However, relatively little is known about how the biosynthesis, assembly and functional diversity of the motor is orchestrated. To address this issue, we have conducted an arrayed CRISPR loss-of-function screen in human cells using the distribution of dynein-tethered peroxisomes and early endosomes as readouts. From a guide RNA library targeting 18,253 genes, 195 validated hits were recovered and parsed into those impacting multiple dynein cargoes and those whose effects are restricted to a subset of cargoes. Clustering of high-dimensional phenotypic fingerprints generated from multiplexed images revealed co-functional genes involved in many cellular processes, including several candidate novel regulators of core dynein functions. Mechanistic analysis of one of these proteins, the RNA-binding protein SUGP1, provides evidence that it promotes cargo trafficking by sustaining functional expression of the dynein activator LIS1. Our dataset represents a rich source of new hypotheses for investigating microtubule-based transport, as well as several other aspects of cellular organisation that were captured by our high-content imaging.
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Affiliation(s)
- Chun Hao Wong
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
- Discovery Biology, Discovery Sciences, AstraZeneca, R&D, Cambridge, CB4 0WG, UK
- Current address: Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Steven W. Wingett
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Chen Qian
- Quantitative Biology, Discovery Sciences, AstraZeneca, R&D, Cambridge, CB4 0WG, UK
| | - J. Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Simon L. Bullock
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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4
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Douthwaite JA, Brown CA, Ferdinand JR, Sharma R, Elliott J, Taylor MA, Malintan NT, Duvoisin H, Hill T, Delpuech O, Orton AL, Pitt H, Kuenzi F, Fish S, Nicholls DJ, Cuthbert A, Richards I, Ratcliffe G, Upadhyay A, Marklew A, Hewitt C, Ross-Thriepland D, Brankin C, Chodorge M, Browne G, Mander PK, DeWildt RM, Weaver S, Smee PA, van Kempen J, Bartlett JG, Allen PM, Koppe EL, Ashby CA, Phipps JD, Mehta N, Brierley DJ, Tew DG, Leveridge MV, Baddeley SM, Goodfellow IG, Green C, Abell C, Neely A, Waddell I, Rees S, Maxwell PH, Pangalos MN, Howes R, Clark R. Improving the efficiency and effectiveness of an industrial SARS-CoV-2 diagnostic facility. Sci Rep 2022; 12:3114. [PMID: 35210470 PMCID: PMC8873195 DOI: 10.1038/s41598-022-06873-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 02/07/2022] [Indexed: 11/24/2022] Open
Abstract
On 11th March 2020, the UK government announced plans for the scaling of COVID-19 testing, and on 27th March 2020 it was announced that a new alliance of private sector and academic collaborative laboratories were being created to generate the testing capacity required. The Cambridge COVID-19 Testing Centre (CCTC) was established during April 2020 through collaboration between AstraZeneca, GlaxoSmithKline, and the University of Cambridge, with Charles River Laboratories joining the collaboration at the end of July 2020. The CCTC lab operation focussed on the optimised use of automation, introduction of novel technologies and process modelling to enable a testing capacity of 22,000 tests per day. Here we describe the optimisation of the laboratory process through the continued exploitation of internal performance metrics, while introducing new technologies including the Heat Inactivation of clinical samples upon receipt into the laboratory and a Direct to PCR protocol that removed the requirement for the RNA extraction step. We anticipate that these methods will have value in driving continued efficiency and effectiveness within all large scale viral diagnostic testing laboratories.
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Affiliation(s)
| | | | - John R Ferdinand
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rahul Sharma
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jane Elliott
- BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | | | | | - Thomas Hill
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | | | | | - Haidee Pitt
- BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Fred Kuenzi
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Simon Fish
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK.,GSK R&D Tech, Stevenage, UK
| | | | | | - Ian Richards
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Giles Ratcliffe
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | | | - Abigail Marklew
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Craig Hewitt
- BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ian G Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Clive Green
- BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Chris Abell
- Vice Chancellor's Office, University of Cambridge, Cambridge, UK
| | - Andy Neely
- Vice Chancellor's Office, University of Cambridge, Cambridge, UK
| | - Ian Waddell
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Steve Rees
- BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | | | - Rob Howes
- BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Roger Clark
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
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5
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Ding M, Malhotra R, Ottosson T, Lundqvist M, Mebrahtu A, Brengdahl J, Gehrmann U, Bäck E, Ross-Thriepland D, Isaksson I, Magnusson B, Sachsenmeier KF, Tegel H, Hober S, Uhlén M, Mayr LM, Davies R, Rockberg J, Schiavone LH. Secretome screening reveals immunomodulating functions of IFNα-7, PAP and GDF-7 on regulatory T-cells. Sci Rep 2021; 11:16767. [PMID: 34408239 PMCID: PMC8373891 DOI: 10.1038/s41598-021-96184-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 08/05/2021] [Indexed: 02/07/2023] Open
Abstract
Regulatory T cells (Tregs) are the key cells regulating peripheral autoreactive T lymphocytes. Tregs exert their function by suppressing effector T cells. Tregs have been shown to play essential roles in the control of a variety of physiological and pathological immune responses. However, Tregs are unstable and can lose the expression of FOXP3 and suppressive functions as a consequence of outer stimuli. Available literature suggests that secreted proteins regulate Treg functional states, such as differentiation, proliferation and suppressive function. Identification of secreted proteins that affect Treg cell function are highly interesting for both therapeutic and diagnostic purposes in either hyperactive or immunosuppressed populations. Here, we report a phenotypic screening of a human secretome library in human Treg cells utilising a high throughput flow cytometry technology. Screening a library of 575 secreted proteins allowed us to identify proteins stabilising or destabilising the Treg phenotype as suggested by changes in expression of Treg marker proteins FOXP3 and/or CTLA4. Four proteins including GDF-7, IL-10, PAP and IFNα-7 were identified as positive regulators that increased FOXP3 and/or CTLA4 expression. PAP is a phosphatase. A catalytic-dead version of the protein did not induce an increase in FOXP3 expression. Ten interferon proteins were identified as negative regulators that reduced the expression of both CTLA4 and FOXP3, without affecting cell viability. A transcriptomics analysis supported the differential effect on Tregs of IFNα-7 versus other IFNα proteins, indicating differences in JAK/STAT signaling. A conformational model experiment confirmed a tenfold reduction in IFNAR-mediated ISG transcription for IFNα-7 compared to IFNα-10. This further strengthened the theory of a shift in downstream messaging upon external stimulation. As a summary, we have identified four positive regulators of FOXP3 and/or CTLA4 expression. Further exploration of these Treg modulators and their method of action has the potential to aid the discovery of novel therapies for both autoimmune and infectious diseases as well as for cancer.
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Affiliation(s)
- Mei Ding
- grid.418151.80000 0001 1519 6403Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Rajneesh Malhotra
- grid.418151.80000 0001 1519 6403Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Tomas Ottosson
- grid.418151.80000 0001 1519 6403Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Magnus Lundqvist
- grid.5037.10000000121581746Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Aman Mebrahtu
- grid.5037.10000000121581746Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Johan Brengdahl
- grid.418151.80000 0001 1519 6403Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Ulf Gehrmann
- grid.418151.80000 0001 1519 6403Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elisabeth Bäck
- grid.418151.80000 0001 1519 6403Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Douglas Ross-Thriepland
- grid.417815.e0000 0004 5929 4381Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Ida Isaksson
- grid.418151.80000 0001 1519 6403Sample Management, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Björn Magnusson
- grid.418151.80000 0001 1519 6403Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Hanna Tegel
- grid.5037.10000000121581746Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Sophia Hober
- grid.5037.10000000121581746Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- grid.5037.10000000121581746Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Lorenz M. Mayr
- grid.417815.e0000 0004 5929 4381Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Rick Davies
- grid.417815.e0000 0004 5929 4381Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Johan Rockberg
- grid.5037.10000000121581746Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Lovisa Holmberg Schiavone
- grid.418151.80000 0001 1519 6403Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
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6
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Guerriero ML, Corrigan A, Bornot A, Firth M, O'Shea P, Ross-Thriepland D, Peel S. Delivering Robust Candidates to the Drug Pipeline through Computational Analysis of Arrayed CRISPR Screens. SLAS Discov 2020; 25:646-654. [PMID: 32394775 DOI: 10.1177/2472555220921132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Genome-wide arrayed CRISPR screening is a powerful method for drug target identification as it enables exploration of the effect of individual gene perturbations using diverse highly multiplexed functional and phenotypic assays. Using high-content imaging, we can measure changes in biomarker expression, intracellular localization, and cell morphology. Here we present the computational pipeline we have developed to support the analysis and interpretation of arrayed CRISPR screens. This includes evaluating the quality of guide RNA libraries, performing image analysis, evaluating assay results quality, data processing, hit identification, ranking, visualization, and biological interpretation.
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Affiliation(s)
- Maria Luisa Guerriero
- Data Sciences & Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Adam Corrigan
- Data Sciences & Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Aurélie Bornot
- Data Sciences & Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Mike Firth
- Data Sciences & Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Patrick O'Shea
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, Cambridgeshire, UK
| | | | - Samantha Peel
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, Cambridgeshire, UK
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7
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Ross-Thriepland D, Bornot A, Butler L, Desai A, Jaiswal H, Peel S, Hunter MR, Odunze U, Isherwood B, Gianni D. Arrayed CRISPR Screening Identifies Novel Targets That Enhance the Productive Delivery of mRNA by MC3-Based Lipid Nanoparticles. SLAS Discov 2020; 25:605-617. [PMID: 32441189 PMCID: PMC7309353 DOI: 10.1177/2472555220925770] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Modified messenger RNAs (mRNAs) hold great potential as therapeutics by using the body’s own processes for protein production. However, a key challenge is efficient delivery of therapeutic mRNA to the cell cytosol and productive protein translation. Lipid nanoparticles (LNPs) are the most clinically advanced system for nucleic acid delivery; however, a relatively narrow therapeutic index makes them unsuitable for many therapeutic applications. A key obstacle to the development of more potent LNPs is a limited mechanistic understanding of the interaction of LNPs with cells. To address this gap, we performed an arrayed CRISPR screen to identify novel pathways important for the functional delivery of MC3 lipid-based LNP encapsulated mRNA (LNP-mRNA). Here, we have developed and validated a robust, high-throughput screening–friendly phenotypic assay to identify novel targets that modulate productive LNP-mRNA delivery. We screened the druggable genome (7795 genes) and validated 44 genes that either increased (37 genes) or inhibited (14 genes) the productive delivery of LNP-mRNA. Many of these genes clustered into families involved with host cell transcription, protein ubiquitination, and intracellular trafficking. We show that both UDP-glucose ceramide glucosyltransferase and V-type proton ATPase can significantly modulate the productive delivery of LNP-mRNA, increasing and decreasing, respectively, with both genetic perturbation and by small-molecule inhibition. Taken together, these findings shed new light into the molecular machinery regulating the delivery of LNPs into cells and improve our mechanistic understanding of the cellular processes modulating the interaction of LNPs with cells.
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Affiliation(s)
| | - Aurelie Bornot
- Quantitative Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
| | - Larissa Butler
- Discovery Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
| | - Arpan Desai
- Advanced Drug Delivery, Pharmaceutical Science, R&D, AstraZeneca, Cambridge, UK
| | - Himjyot Jaiswal
- Discovery Biology, Discovery Science, R&D, AstraZeneca, Molndal, Sweden
| | - Samantha Peel
- Discovery Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
| | - Morag Rose Hunter
- Discovery Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
| | - Uchechukwu Odunze
- Advanced Drug Delivery, Pharmaceutical Science, R&D, AstraZeneca, Cambridge, UK
| | | | - Davide Gianni
- Discovery Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
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8
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Abstract
The hepatitis C virus non-structural 5A (NS5A) protein is highly phosphorylated and plays roles in both virus genome replication and assembly of infectious virus particles. NS5A comprises three domains separated by low complexity sequences (LCS). Mass spectrometry analysis of NS5A revealed the existence of a singly phosphorylated tryptic peptide corresponding to the end of LCS I and the beginning of domain II that contained a number of potential phosphorylatable residues (serines and threonines). Here we use a mutagenic approach to investigate the potential role of three of these threonine residues. Phosphomimetic mutations of two of these (T242E and T244E) resulted in significant reductions in virus genome replication and the production of infectious virus, suggesting that the phosphorylation of these residues negatively regulated virus RNA synthesis. Mutation of T245 had no effect, however when T245E was combined with the other two phosphomimetic mutations (TripleE) the inhibitory effect on replication was less pronounced. Effects of the mutations on the ratio of basally/hyperphosphorylated NS5A, together with the apparent molecular weight of the basally phosphorylated species were also observed. Lastly, two of the mutations (T245A and TripleE) resulted in a perinuclear restricted localization of NS5A. These data add further complexity to NS5A phosphorylation and suggest that this analysis be extended outwith the serine-rich cluster within LCS I.
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Affiliation(s)
- Niluka Goonawardane
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Douglas Ross-Thriepland
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Present address: AstraZeneca, Cambridge Biomedical Campus, Cambridge, CB20AA, UK
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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9
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Stewart H, Bartlett C, Ross-Thriepland D, Shaw J, Griffin S, Harris M. A novel method for the measurement of hepatitis C virus infectious titres using the IncuCyte ZOOM and its application to antiviral screening. J Virol Methods 2015; 218:59-65. [PMID: 25796989 PMCID: PMC4411217 DOI: 10.1016/j.jviromet.2015.03.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 12/31/2022]
Abstract
Hepatitis C virus (HCV) is a significant human pathogen, causing severe liver disease. Accurate quantification of viral titres is essential for the majority of assays. The current methods of HCV titration and quantification are laborious and imprecise. We report a novel method for calculating infectious HCV titres using the IncuCyte ZOOM. This method has applications for screening of novel antiviral compounds.
Hepatitis C virus (HCV) is a significant human pathogen infecting 3% of the world population. An infectious molecular clone capable of replicating and releasing infectious virions in cell culture has only been available since 2005, leaving a significant knowledge gap concerning post-RNA replication events such as particle assembly, trafficking and release. Thus, a fast, efficient and accurate method of measuring infectious viral titres is highly desirable. Current methods rely upon manual counting of infected cell foci and so are both labour-intensive and susceptible to human error. Here, we report a novel protocol, which utilises the IncuCyte ZOOM instrument and related software to accurately count infected cells and extrapolation of this data to produce an infectious titre, reported as infectious units per millilitre (IU/mL). This method reduces cost, time and error in experiments. We also demonstrate that this approach is amenable to high-throughput compound screening, thereby expediting the identification of novel antivirals.
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Affiliation(s)
- Hazel Stewart
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Christopher Bartlett
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Douglas Ross-Thriepland
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Joseph Shaw
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom
| | - Stephen Griffin
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.
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10
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Abstract
Since one of us co-authored a review on NS5A a decade ago, the hepatitis C virus (HCV) field has changed dramatically, primarily due to the advent of the JFH-1 cell culture infectious clone, which allowed the study of all aspects of the virus life cycle from entry to exit. This review will describe advances in our understanding of NS5A biology over the past decade, highlighting how the JFH-1 system has allowed us to determine that NS5A is essential not only in genome replication but also in the assembly of infectious virions. We shall review the recent structural insights - NS5A is predicted to comprise three domains; X-ray crystallography has revealed the structure of domain I but there is a lack of detailed structural information about the other two domains, which are predicted to be largely unstructured. Recent insights into the phosphorylation of NS5A will be discussed, and we shall highlight a few pertinent examples from the ever-expanding list of NS5A-binding partners identified over the past decade. Lastly, we shall review the literature showing that NS5A is a potential target for a new class of highly potent small molecules that function to inhibit virus replication. These direct-acting antivirals (DAAs) are now either licensed, or in the late stages of approval for clinical use both in the USA and in the UK/Europe. In combination with other DAAs targeting the viral protease (NS3) and polymerase (NS5B), they are revolutionizing treatment for HCV infection.
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Affiliation(s)
- Douglas Ross-Thriepland
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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Ross-Thriepland D, Amako Y, Harris M. The C terminus of NS5A domain II is a key determinant of hepatitis C virus genome replication, but is not required for virion assembly and release. J Gen Virol 2013; 94:1009-1018. [PMID: 23324467 PMCID: PMC3709587 DOI: 10.1099/vir.0.050633-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 01/11/2013] [Indexed: 12/12/2022] Open
Abstract
The NS5A protein of hepatitis C virus (HCV) plays roles in both virus genome replication and the assembly of infectious virus particles. NS5A comprises three domains, separated by low-complexity sequences. Whilst the function of domain I appears to be predominantly involved with genome replication, the roles of domains II and III are less well defined. It has been reported previously that a deletion spanning the majority of domain II but retaining the C-terminal 35 residues had no effect on virus production; however, deletion of the entire domain II eliminated genome replication, pointing to a key role for the C terminus of this domain. Recent work has also highlighted this region as the potential binding site of the host factor cyclophilin A (CypA). To define this requirement for replication in more detail, and to investigate the involvement of CypA, we conducted a mutagenic study of the C-terminal 30 residues of domain II within the context of both the infectious JFH-1 virus and a JFH-1-derived subgenomic replicon. We showed that 12 of these residues were absolutely required for virus genome replication, whilst mutations of the remainder either had no phenotype or exhibited a partial reduction in genome replication. There was an absolute correlation between the datasets for virus and subgenomic replicon, indicating that this region is involved solely in the process of genome replication. Comparison of our data with a previously published analysis of the same region in genotype 1b revealed some important differences between the two genotypes of HCV.
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Affiliation(s)
- Douglas Ross-Thriepland
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Yutaka Amako
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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