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Pearson GJ, Mears HV, Broncel M, Snijders AP, Bauer DLV, Carlton JG. ER-export and ARFRP1/AP-1-dependent delivery of SARS-CoV-2 Envelope to lysosomes controls late stages of viral replication. Sci Adv 2024; 10:eadl5012. [PMID: 38569033 PMCID: PMC10990277 DOI: 10.1126/sciadv.adl5012] [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] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
The β-coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the global COVID-19 pandemic. Coronaviral Envelope (E) proteins are pentameric viroporins that play essential roles in assembly, release, and pathogenesis. We developed a nondisruptive tagging strategy for SARS-CoV-2 E and find that, at steady state, it localizes to the Golgi and to lysosomes. We identify sequences in E, conserved across Coronaviridae, responsible for endoplasmic reticulum-to-Golgi export, and relate this activity to interaction with COP-II via SEC24. Using proximity biotinylation, we identify an ADP ribosylation factor 1/adaptor protein-1 (ARFRP1/AP-1)-dependent pathway allowing Golgi-to-lysosome trafficking of E. We identify sequences in E that bind AP-1, are conserved across β-coronaviruses, and allow E to be trafficked from Golgi to lysosomes. We show that E acts to deacidify lysosomes and, by developing a trans-complementation assay for SARS-CoV-2 structural proteins, that lysosomal delivery of E and its viroporin activity is necessary for efficient viral replication and release.
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Affiliation(s)
- Guy J. Pearson
- Organelle Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- School of Cancer & Pharmaceutical Sciences, King’s College London, Great Maze Pond, London SE1 1UL, UK
| | - Harriet V. Mears
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Malgorzata Broncel
- Proteomic Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P. Snijders
- Proteomic Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David L. V. Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jeremy G. Carlton
- Organelle Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- School of Cancer & Pharmaceutical Sciences, King’s College London, Great Maze Pond, London SE1 1UL, UK
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2
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Shawe-Taylor M, Greenwood D, Hobbs A, Dowgier G, Penn R, Sanderson T, Stevenson-Leggett P, Bazire J, Harvey R, Libri V, Kassiotis G, Gamblin S, Lewis NS, Williams B, Swanton C, Gandhi S, Carr EJ, Wu MY, Bauer DLV, Wall EC. Divergent performance of vaccines in the UK autumn 2023 COVID-19 booster campaign. Lancet 2024; 403:1133-1136. [PMID: 38484752 DOI: 10.1016/s0140-6736(24)00316-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/25/2024]
Affiliation(s)
- Marianne Shawe-Taylor
- The Francis Crick Institute, London NW1 1AT, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | | | | | | | | | | | | | | | - Ruth Harvey
- Worldwide Influenza Centre, London NW1 1AT, UK
| | - Vincenzo Libri
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | - George Kassiotis
- The Francis Crick Institute, London NW1 1AT, UK; Department of Infectious Disease, St Mary's Hospital, Imperial College London, London, UK
| | | | | | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK; University College London, London, UK
| | - Charles Swanton
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Sonia Gandhi
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Edward J Carr
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Mary Y Wu
- The Francis Crick Institute, London NW1 1AT, UK
| | - David L V Bauer
- The Francis Crick Institute, London NW1 1AT, UK; Genotype-to-Phenotype 2 Consortium (G2P2-UK), UK
| | - Emma C Wall
- The Francis Crick Institute, London NW1 1AT, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK.
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3
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Townsley H, Gahir J, Russell TW, Greenwood D, Carr EJ, Dyke M, Adams L, Miah M, Clayton B, Smith C, Miranda M, Mears HV, Bailey C, Black JRM, Fowler AS, Crawford M, Wilkinson K, Hutchinson M, Harvey R, O’Reilly N, Kelly G, Goldstone R, Beale R, Papineni P, Corrah T, Gilson R, Caidan S, Nicod J, Gamblin S, Kassiotis G, Libri V, Williams B, Gandhi S, Kucharski AJ, Swanton C, Bauer DLV, Wall EC. COVID-19 in non-hospitalised adults caused by either SARS-CoV-2 sub-variants Omicron BA.1, BA.2, BA.4/5 or Delta associates with similar illness duration, symptom severity and viral kinetics, irrespective of vaccination history. PLoS One 2024; 19:e0294897. [PMID: 38512960 PMCID: PMC10956747 DOI: 10.1371/journal.pone.0294897] [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: 03/10/2023] [Accepted: 11/11/2023] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND SARS-CoV-2 variant Omicron rapidly evolved over 2022, causing three waves of infection due to sub-variants BA.1, BA.2 and BA.4/5. We sought to characterise symptoms and viral loads over the course of COVID-19 infection with these sub-variants in otherwise-healthy, vaccinated, non-hospitalised adults, and compared data to infections with the preceding Delta variant of concern (VOC). METHODS In a prospective, observational cohort study, healthy vaccinated UK adults who reported a positive polymerase chain reaction (PCR) or lateral flow test, self-swabbed on alternate weekdays until day 10. We compared participant-reported symptoms and viral load trajectories between infections caused by VOCs Delta and Omicron (sub-variants BA.1, BA.2 or BA.4/5), and tested for relationships between vaccine dose, symptoms and PCR cycle threshold (Ct) as a proxy for viral load using Chi-squared (χ2) and Wilcoxon tests. RESULTS 563 infection episodes were reported among 491 participants. Across infection episodes, there was little variation in symptom burden (4 [IQR 3-5] symptoms) and duration (8 [IQR 6-11] days). Whilst symptom profiles differed among infections caused by Delta compared to Omicron sub-variants, symptom profiles were similar between Omicron sub-variants. Anosmia was reported more frequently in Delta infections after 2 doses compared with Omicron sub-variant infections after 3 doses, for example: 42% (25/60) of participants with Delta infection compared to 9% (6/67) with Omicron BA.4/5 (χ2 P < 0.001; OR 7.3 [95% CI 2.7-19.4]). Fever was less common with Delta (20/60 participants; 33%) than Omicron BA.4/5 (39/67; 58%; χ2 P = 0.008; OR 0.4 [CI 0.2-0.7]). Amongst infections with an Omicron sub-variants, symptoms of coryza, fatigue, cough and myalgia predominated. Viral load trajectories and peaks did not differ between Delta, and Omicron, irrespective of symptom severity (including asymptomatic participants), VOC or vaccination status. PCR Ct values were negatively associated with time since vaccination in participants infected with BA.1 (β = -0.05 (CI -0.10-0.01); P = 0.031); however, this trend was not observed in BA.2 or BA.4/5 infections. CONCLUSION Our study emphasises both the changing symptom profile of COVID-19 infections in the Omicron era, and ongoing transmission risk of Omicron sub-variants in vaccinated adults. TRIAL REGISTRATION NCT04750356.
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Affiliation(s)
- Hermaleigh Townsley
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Joshua Gahir
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Timothy W. Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | | | - Matala Dyke
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Lorin Adams
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Murad Miah
- The Francis Crick Institute, London, United Kingdom
| | | | - Callie Smith
- The Francis Crick Institute, London, United Kingdom
| | | | | | - Chris Bailey
- The Francis Crick Institute, London, United Kingdom
| | - James R. M. Black
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | | | | | | | | | - Ruth Harvey
- The Francis Crick Institute, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | | | - Gavin Kelly
- The Francis Crick Institute, London, United Kingdom
| | | | - Rupert Beale
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | | | - Tumena Corrah
- London Northwest University Healthcare NHS Trust, London, United Kingdom
| | - Richard Gilson
- Camden and North West London NHS Community Trust, London, United Kingdom
| | - Simon Caidan
- The Francis Crick Institute, London, United Kingdom
| | - Jerome Nicod
- The Francis Crick Institute, London, United Kingdom
| | | | - George Kassiotis
- The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, St Mary’s Hospital, Imperial College London, London, United Kingdom
| | - Vincenzo Libri
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Sonia Gandhi
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Charles Swanton
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - David L. V. Bauer
- The Francis Crick Institute, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | - Emma C. Wall
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
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4
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Carr EJ, Dowgier G, Greenwood D, Herman LS, Hobbs A, Ragno M, Stevenson-Leggett P, Gahir J, Townsley H, Harvey R, Bailey C, Fowler AS, Miah M, Smith C, Miranda M, Bawumia P, Mears HV, Adams L, Hatipoglu E, O'Reilly N, Warchal S, Sawyer C, Ambrose K, Strange A, Kelly G, Beale R, Papineni P, Corrah T, Gilson R, Gamblin S, Kassiotis G, Libri V, Williams B, Swanton C, Gandhi S, Bauer DLV, Wall E, Wu MY. SARS-CoV-2 mucosal neutralising immunity after vaccination. Lancet Infect Dis 2024; 24:e4-e5. [PMID: 38070528 DOI: 10.1016/s1473-3099(23)00705-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/30/2023] [Accepted: 11/08/2023] [Indexed: 12/24/2023]
Affiliation(s)
- Edward J Carr
- UCL Department of Renal Medicine, Royal Free Hospital, Rowland Hill Street, London, UK; The Francis Crick Institute, London NW1 1AT, UK
| | | | | | | | | | | | | | - Joshua Gahir
- The Francis Crick Institute, London NW1 1AT, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | | | - Ruth Harvey
- Worldwide Influenza Centre, London NW1 1AT, UK
| | | | | | - Murad Miah
- The Francis Crick Institute, London NW1 1AT, UK
| | | | | | | | | | - Lorin Adams
- Worldwide Influenza Centre, London NW1 1AT, UK
| | - Emine Hatipoglu
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | | | | | | | | | - Amy Strange
- The Francis Crick Institute, London NW1 1AT, UK
| | - Gavin Kelly
- The Francis Crick Institute, London NW1 1AT, UK
| | - Rupert Beale
- The Francis Crick Institute, London NW1 1AT, UK; The Francis Crick Institute, London NW1 1AT, UK; Genotype-to-Phenotype UK National Virology Consortium, London, UK
| | | | - Tumena Corrah
- London Northwest University Healthcare NHS Trust, London, UK
| | - Richard Gilson
- Central and North West London NHS Foundation Trust, London, UK; University College London, London, UK
| | | | - George Kassiotis
- The Francis Crick Institute, London NW1 1AT, UK; Department of Infectious Disease, St Mary's Hospital, Imperial College London, London, UK
| | - Vincenzo Libri
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK; University College London, London, UK
| | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK; University College London, London, UK
| | - Charles Swanton
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Sonia Gandhi
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - David L V Bauer
- The Francis Crick Institute, London NW1 1AT, UK; Genotype-to-Phenotype UK National Virology Consortium, London, UK
| | - Emma Wall
- The Francis Crick Institute, London NW1 1AT, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | - Mary Y Wu
- COVID Surveillance Unit, London NW1 1AT, UK; The Francis Crick Institute, London NW1 1AT, UK.
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5
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Russell TW, Townsley H, Abbott S, Hellewell J, Carr EJ, Chapman LAC, Pung R, Quilty BJ, Hodgson D, Fowler AS, Adams L, Bailey C, Mears HV, Harvey R, Clayton B, O’Reilly N, Ngai Y, Nicod J, Gamblin S, Williams B, Gandhi S, Swanton C, Beale R, Bauer DLV, Wall EC, Kucharski AJ. Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants. PLoS Biol 2024; 22:e3002463. [PMID: 38289907 PMCID: PMC10826969 DOI: 10.1371/journal.pbio.3002463] [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: 03/25/2023] [Accepted: 12/07/2023] [Indexed: 02/01/2024] Open
Abstract
The emergence of successive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) during 2020 to 2022, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need to understand the drivers of such growth. However, both pathogen biology and changing host characteristics-such as varying levels of immunity-can combine to influence replication and transmission of SARS-CoV-2 within and between hosts. Disentangling the role of variant and host in individual-level viral shedding of VOCs is essential to inform Coronavirus Disease 2019 (COVID-19) planning and response and interpret past epidemic trends. Using data from a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening, we developed a Bayesian hierarchical model to reconstruct individual-level viral kinetics and estimate how different factors shaped viral dynamics, measured by PCR cycle threshold (Ct) values over time. Jointly accounting for both interindividual variation in Ct values and complex host characteristics-such as vaccination status, exposure history, and age-we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least 5 prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups. Our findings illustrate the value of linking information on participant characteristics, symptom profile and infecting variant with prospective PCR sampling, and the importance of accounting for increasingly complex population exposure landscapes when analysing the viral kinetics of VOCs. Trial Registration: The Legacy study is a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening for SARS-CoV-2 at University College London Hospitals or at the Francis Crick Institute (NCT04750356) (22,23). The Legacy study was approved by London Camden and Kings Cross Health Research Authority Research and Ethics committee (IRAS number 286469). The Legacy study was approved by London Camden and Kings Cross Health Research Authority Research and Ethics committee (IRAS number 286469) and is sponsored by University College London Hospitals. Written consent was given by all participants.
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Affiliation(s)
- Timothy W. Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Hermaleigh Townsley
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Sam Abbott
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Joel Hellewell
- European Molecular Biology Laboratory-European Bioinformatics Institute, Cambridge, United Kingdom
| | - Edward J. Carr
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Lloyd A. C. Chapman
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Lancaster University, Bailrigg, Lancaster, United Kingdom
| | - Rachael Pung
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Billy J. Quilty
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - David Hodgson
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Lorin Adams
- The Francis Crick Institute, London, United Kingdom
| | - Chris Bailey
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | | | - Ruth Harvey
- The Francis Crick Institute, London, United Kingdom
| | | | | | - Yenting Ngai
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Jerome Nicod
- The Francis Crick Institute, London, United Kingdom
| | | | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- University College London, London, United Kingdom
| | - Sonia Gandhi
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Charles Swanton
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Rupert Beale
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK), London, United Kingdom
| | - David L. V. Bauer
- The Francis Crick Institute, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK), London, United Kingdom
| | - Emma C. Wall
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- University College London, London, United Kingdom
| | - Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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6
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Bailey C, Sanderson T, Townsley H, Goldman J, Black JRM, Young G, Goldstone R, Fowler AS, Ward S, Jackson DJ, Cubitt L, Dearing V, O'Neil O, Crawford M, Snell D, Finadis M, Edwards A, Perez-Lloret J, Gahir J, Carr EJ, Riddell A, Aitken J, Ambrose K, Sawyer C, O'Reilly N, Caidan S, Wu MY, Walker PA, Hindmarsh S, Howell M, Jordan A, Fleming J, Houlihan C, Nastouli E, Moores R, Hsu D, Papineni P, Corrah T, Gilson R, MacRae J, Hubank M, Van As N, Turajlic S, Beale R, Levi M, Barrell S, Williams B, Gamblin S, Nicod J, Gandhi S, Bauer DLV, Wall EC, Swanton C. Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London. Lancet 2023; 402:21-24. [PMID: 37348521 PMCID: PMC10278995 DOI: 10.1016/s0140-6736(23)00917-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/15/2023] [Accepted: 05/02/2023] [Indexed: 06/24/2023]
Affiliation(s)
- Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK; University College London, London, UK
| | - Theo Sanderson
- Malaria Biochemistry Laboratory, London NW1 1AT, UK; COVID-19 Genomics UK Consortium, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Hermaleigh Townsley
- Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK
| | | | - James R M Black
- Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; University College London, London, UK
| | - George Young
- Applied Biotechnology Laboratory, London NW1 1AT, UK
| | - Robert Goldstone
- Advanced Sequencing Facility, London NW1 1AT, UK; Bioinformatics and Biostatistics STP, London NW1 1AT, UK
| | | | - Sophia Ward
- Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; Advanced Sequencing Facility, London NW1 1AT, UK
| | | | - Laura Cubitt
- Advanced Sequencing Facility, London NW1 1AT, UK
| | | | - Olga O'Neil
- Advanced Sequencing Facility, London NW1 1AT, UK
| | | | - Daniel Snell
- Advanced Sequencing Facility, London NW1 1AT, UK
| | | | | | | | - Joshua Gahir
- Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK
| | - Edward J Carr
- Cell Biology of Infection Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK
| | | | - Jim Aitken
- Information Technology Office, London NW1 1AT, UK
| | | | | | | | | | - Mary Y Wu
- COVID Surveillance Unit, London NW1 1AT, UK
| | | | | | | | | | | | | | - Eleni Nastouli
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Desmond Hsu
- Royal Free London NHS Foundation Trust, London, UK
| | | | - Tumena Corrah
- London Northwest University Healthcare NHS Trust, London, UK
| | - Richard Gilson
- Central and Northwest London NHS Foundation Trust, London, UK
| | | | - Michael Hubank
- Royal Marsden Hospitals NHS Foundation Trust, London, UK
| | | | | | - Rupert Beale
- Cell Biology of Infection Laboratory, London NW1 1AT, UK; University College London, London, UK; Genotype to Phenotype Consortium UK, Imperial College London, London, UK
| | - Marcel Levi
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Bryan Williams
- University College London Hospitals NHS Foundation Trust, London, UK; University College London, London, UK
| | | | - Jerome Nicod
- Advanced Sequencing Facility, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK
| | - Sonia Gandhi
- Neurodegeneration Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - David L V Bauer
- RNA Virus Replication Laboratory, London NW1 1AT, UK; Genotype to Phenotype Consortium UK, Imperial College London, London, UK
| | - Emma C Wall
- Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK; University College London, London, UK
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7
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Wu MY, Shepherd STC, Fendler A, Carr EJ, Au L, Harvey R, Dowgier G, Hobbs A, Herman LS, Ragno M, Adams L, Schmitt AM, Tippu Z, Shum B, Farag S, Rogiers A, O'Reilly N, Bawumia P, Smith C, Carlyle E, Edmonds K, Del Rosario L, Lingard K, Mangwende M, Holt L, Ahmod H, Korteweg J, Foley T, Barber T, Hepworth S, Emslie-Henry A, Caulfield-Lynch N, Byrne F, Deng D, Williams B, Brown M, Caidan S, Gavrielides M, MacRae JI, Kelly G, Peat K, Kelly D, Murra A, Kelly K, O'Flaherty M, Popat S, Yousaf N, Jhanji S, Tatham K, Cunningham D, Van As N, Young K, Furness AJS, Pickering L, Beale R, Swanton C, Gandhi S, Gamblin S, Bauer DLV, Kassiotis G, Howell M, Walker S, Nicholson E, Larkin J, Wall EC, Turajlic S. Sotrovimab restores neutralization against current Omicron subvariants in patients with blood cancer. Cancer Cell 2023; 41:821-823. [PMID: 37116490 PMCID: PMC10113515 DOI: 10.1016/j.ccell.2023.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/30/2023]
Abstract
Wu et al. report that patients with hematologic malignancies have reduced immunity against SARS-CoV-2 Omicron subvariants and Sotrovimab retains neutralizing capacity against all tested Omicron subvariants.
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Affiliation(s)
- Mary Y Wu
- COVID Surveillance Unit, The Francis Crick Institute, London NW1 1AT, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK
| | - Annika Fendler
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Department of Urology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Edward J Carr
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Division of Medicine, University College London, London NW1 2PG, UK
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK; Department of Medical Oncology, Peter MacCallum Cancer Centre, VIC 3010, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, VIC 3010, Melbourne, Australia
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Giulia Dowgier
- COVID Surveillance Unit, The Francis Crick Institute, London NW1 1AT, UK
| | - Agnieszka Hobbs
- COVID Surveillance Unit, The Francis Crick Institute, London NW1 1AT, UK
| | - Lou S Herman
- COVID Surveillance Unit, The Francis Crick Institute, London NW1 1AT, UK
| | - Martina Ragno
- COVID Surveillance Unit, The Francis Crick Institute, London NW1 1AT, UK
| | - Lorin Adams
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Andreas M Schmitt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Zayd Tippu
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK
| | - Benjamin Shum
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK
| | - Sheima Farag
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Aljosja Rogiers
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Nicola O'Reilly
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip Bawumia
- Human Biology Science and Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Callie Smith
- Human Biology Science and Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Eleanor Carlyle
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Kim Edmonds
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lyra Del Rosario
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Karla Lingard
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Mary Mangwende
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lucy Holt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Hamid Ahmod
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Justine Korteweg
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Tara Foley
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Taja Barber
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Stephanie Hepworth
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | | | | | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Daqi Deng
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Bryan Williams
- School of Life and Medical Sciences, University College London, 235 Euston Road, London NW1 2BU, UK; University College London Hospitals NHS Foundation Trust Biomedical Research Centre, London WC1E 6BT, UK
| | - Michael Brown
- University College London Hospitals NHS Foundation Trust Biomedical Research Centre, London WC1E 6BT, UK; Clinical Research Department, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Simon Caidan
- Safety, Health & Sustainability, The Francis Crick Institute, London NW1 1AT, UK
| | - Mike Gavrielides
- Scientific Computing Scientific Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - James I MacRae
- Metabolomics Scientific Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Gavin Kelly
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Kema Peat
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Denise Kelly
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Aida Murra
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Kayleigh Kelly
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Molly O'Flaherty
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Sanjay Popat
- Lung Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Nadia Yousaf
- Lung Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Shaman Jhanji
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Kate Tatham
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - David Cunningham
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey, SM2 5PT, UK
| | - Nicholas Van As
- Clincal Oncology Unit, The Royal Marsden NHS Foundation Trust, London NW1 1AT, UK
| | - Kate Young
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Andrew J S Furness
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK
| | - Lisa Pickering
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Division of Medicine, University College London, London NW1 2PG, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK; University College London Cancer Institute, London WC1E 6DD, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Steve Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - David L V Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Susanna Walker
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Emma Nicholson
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Haemato-oncology Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - James Larkin
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK
| | - Emma C Wall
- School of Life and Medical Sciences, University College London, 235 Euston Road, London NW1 2BU, UK; The Francis Crick Institute, London NW1 1AT, UK.
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK.
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8
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Wu MY, Carr EJ, Harvey R, Mears HV, Kjaer S, Townsley H, Hobbs A, Ragno M, Herman LS, Adams L, Gamblin S, Howell M, Beale R, Brown M, Williams B, Gandhi S, Swanton C, Wall EC, Bauer DLV. WHO's Therapeutics and COVID-19 Living Guideline on mAbs needs to be reassessed. Lancet 2022; 400:2193-2196. [PMID: 36209762 PMCID: PMC9536776 DOI: 10.1016/s0140-6736(22)01938-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 01/26/2023]
Affiliation(s)
- Mary Y Wu
- The Francis Crick Institute, London NW1 1AT, UK
| | | | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London, UK
| | | | - Svend Kjaer
- The Francis Crick Institute, London NW1 1AT, UK
| | - Hermaleigh Townsley
- The Francis Crick Institute, London NW1 1AT, UK; Worldwide Influenza Centre, The Francis Crick Institute, London, UK
| | | | | | | | - Lorin Adams
- Worldwide Influenza Centre, The Francis Crick Institute, London, UK
| | | | | | | | - Michael Brown
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK; University College London, London, UK
| | - Sonia Gandhi
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Charles Swanton
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Emma C Wall
- The Francis Crick Institute, London NW1 1AT, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
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9
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Fendler A, Shepherd STC, Au L, Wu M, Harvey R, Wilkinson KA, Schmitt AM, Tippu Z, Shum B, Farag S, Rogiers A, Carlyle E, Edmonds K, Del Rosario L, Lingard K, Mangwende M, Holt L, Ahmod H, Korteweg J, Foley T, Barber T, Emslie-Henry A, Caulfield-Lynch N, Byrne F, Deng D, Kjaer S, Song OR, Queval CJ, Kavanagh C, Wall EC, Carr EJ, Caidan S, Gavrielides M, MacRae JI, Kelly G, Peat K, Kelly D, Murra A, Kelly K, O'Flaherty M, Shea RL, Gardner G, Murray D, Popat S, Yousaf N, Jhanji S, Tatham K, Cunningham D, Van As N, Young K, Furness AJS, Pickering L, Beale R, Swanton C, Gandhi S, Gamblin S, Bauer DLV, Kassiotis G, Howell M, Nicholson E, Walker S, Wilkinson RJ, Larkin J, Turajlic S. Functional immune responses against SARS-CoV-2 variants of concern after fourth COVID-19 vaccine dose or infection in patients with blood cancer. Cell Rep Med 2022; 3:100781. [PMID: 36240755 PMCID: PMC9513326 DOI: 10.1016/j.xcrm.2022.100781] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/07/2022] [Accepted: 09/21/2022] [Indexed: 11/28/2022]
Abstract
Patients with blood cancer continue to have a greater risk of inadequate immune responses following three COVID-19 vaccine doses and risk of severe COVID-19 disease. In the context of the CAPTURE study (NCT03226886), we report immune responses in 80 patients with blood cancer who received a fourth dose of BNT162b2. We measured neutralizing antibody titers (NAbTs) using a live virus microneutralization assay against wild-type (WT), Delta, and Omicron BA.1 and BA.2 and T cell responses against WT and Omicron BA.1 using an activation-induced marker (AIM) assay. The proportion of patients with detectable NAb titers and T cell responses after the fourth vaccine dose increased compared with that after the third vaccine dose. Patients who received B cell-depleting therapies within the 12 months before vaccination have the greatest risk of not having detectable NAbT. In addition, we report immune responses in 57 patients with breakthrough infections after vaccination.
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Affiliation(s)
- Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Mary Wu
- COVID Surveillance Unit, The Francis Crick Institute, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Katalin A Wilkinson
- Tuberculosis Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Wellcome Center for Infectious Disease Research in Africa, University of Cape Town, Observatory 7925, Republic of South Africa
| | - Andreas M Schmitt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Zayd Tippu
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Benjamin Shum
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Sheima Farag
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Aljosja Rogiers
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Eleanor Carlyle
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Kim Edmonds
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lyra Del Rosario
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Karla Lingard
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Mary Mangwende
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lucy Holt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Hamid Ahmod
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Justine Korteweg
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Tara Foley
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Taja Barber
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | | | | | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Daqi Deng
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjaer
- Structural Biology Scientific Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Ok-Ryul Song
- High Throughput Screening Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Christophe J Queval
- High Throughput Screening Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Caitlin Kavanagh
- COVID Surveillance Unit, The Francis Crick Institute, London NW1 1AT, UK
| | - Emma C Wall
- High Throughput Screening Laboratory, The Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust Biomedical Research Centre, London WC1E 6BT, UK
| | - Edward J Carr
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Simon Caidan
- Safety, Health & Sustainability, The Francis Crick Institute, London NW1 1AT, UK
| | - Mike Gavrielides
- Scientific Computing Scientific Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - James I MacRae
- Metabolomics Scientific Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Gavin Kelly
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Kema Peat
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Denise Kelly
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Aida Murra
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Kayleigh Kelly
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Molly O'Flaherty
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Robyn L Shea
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London NW1 1AT, UK; Translational Cancer Biochemistry Laboratory, The Institute of Cancer Research, London SW7 3RP, UK
| | - Gail Gardner
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London NW1 1AT, UK
| | - Darren Murray
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London NW1 1AT, UK
| | - Sanjay Popat
- Lung Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Nadia Yousaf
- Lung Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Shaman Jhanji
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Kate Tatham
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - David Cunningham
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK
| | - Nicholas Van As
- Clincal Oncology Unit, The Royal Marsden NHS Foundation Trust, London NW1 1AT, UK
| | - Kate Young
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Andrew J S Furness
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lisa Pickering
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Division of Medicine, University College London, London NW1 2PG, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK; University College London Cancer Institute, London WC1E 6DD, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Steve Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - David L V Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Emma Nicholson
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Haemato-oncology Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - Susanna Walker
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Robert J Wilkinson
- Tuberculosis Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Wellcome Center for Infectious Disease Research in Africa, University of Cape Town, Observatory 7925, Republic of South Africa; Department of Infectious Disease, Imperial College London, London W2 0NN, UK
| | - James Larkin
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK.
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10
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Ng KW, Faulkner N, Finsterbusch K, Wu M, Harvey R, Hussain S, Greco M, Liu Y, Kjaer S, Swanton C, Gandhi S, Beale R, Gamblin SJ, Cherepanov P, McCauley J, Daniels R, Howell M, Arase H, Wack A, Bauer DLV, Kassiotis G. SARS-CoV-2 S2-targeted vaccination elicits broadly neutralizing antibodies. Sci Transl Med 2022; 14:eabn3715. [PMID: 35895836 DOI: 10.1126/scitranslmed.abn3715] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [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] [Indexed: 12/15/2022]
Abstract
Several variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged during the current coronavirus disease 2019 (COVID-19) pandemic. Although antibody cross-reactivity with the spike glycoproteins (S) of diverse coronaviruses, including endemic common cold coronaviruses (HCoVs), has been documented, it remains unclear whether such antibody responses, typically targeting the conserved S2 subunit, contribute to protection when induced by infection or through vaccination. Using a mouse model, we found that prior HCoV-OC43 S-targeted immunity primes neutralizing antibody responses to otherwise subimmunogenic SARS-CoV-2 S exposure and promotes S2-targeting antibody responses. Moreover, vaccination with SARS-CoV-2 S2 elicited antibodies in mice that neutralized diverse animal and human alphacoronaviruses and betacoronaviruses in vitro and provided a degree of protection against SARS-CoV-2 challenge in vivo. Last, in mice with a history of SARS-CoV-2 Wuhan-based S vaccination, further S2 vaccination induced broader neutralizing antibody response than booster Wuhan S vaccination, suggesting that it may prevent repertoire focusing caused by repeated homologous vaccination. These data establish the protective value of an S2-targeting vaccine and support the notion that S2 vaccination may better prepare the immune system to respond to the changing nature of the S1 subunit in SARS-CoV-2 variants of concern, as well as to future coronavirus zoonoses.
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Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Katja Finsterbusch
- Immunoregulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mary Wu
- High Throughput Screening STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Maria Greco
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Yafei Liu
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan
| | - Svend Kjaer
- Structural Biology STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Sonia Gandhi
- Neurodegradation Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter Cherepanov
- Chromatin structure and mobile DNA Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - John McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rodney Daniels
- Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening STP, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
- Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
| | - Andreas Wack
- Immunoregulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David L V Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Infectious Disease, St Mary's Hospital, Imperial College London, London W2 1PG, UK
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11
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Diefenbacher M, Tan TJC, Bauer DLV, Stadtmueller BM, Wu NC, Brooke CB. Interactions between Influenza A Virus Nucleoprotein and Gene Segment Untranslated Regions Facilitate Selective Modulation of Viral Gene Expression. J Virol 2022; 96:e0020522. [PMID: 35467364 PMCID: PMC9131868 DOI: 10.1128/jvi.00205-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/29/2022] [Indexed: 11/20/2022] Open
Abstract
The influenza A virus (IAV) genome is divided into eight negative-sense, single-stranded RNA segments. Each segment exhibits a unique level and temporal pattern of expression; however, the exact mechanisms underlying the patterns of individual gene segment expression are poorly understood. We previously demonstrated that a single substitution in the viral nucleoprotein (NP:F346S) selectively modulates neuraminidase (NA) gene segment expression while leaving other segments largely unaffected. Given what is currently known about NP function, there is no obvious explanation for how changes in NP can selectively modulate the replication of individual gene segments. In this study, we found that the specificity of this effect for the NA segment is virus strain specific and depends on the untranslated region (UTR) sequences of the NA segment. While the NP:F346S substitution did not significantly alter the RNA binding or oligomerization activities of NP in vitro, it specifically decreased the ability of NP to promote NA segment viral RNA (vRNA) synthesis. In addition to NP residue F346, we identified two other adjacent aromatic residues in NP (Y385 and F479) capable of similarly regulating NA gene segment expression, suggesting a larger role for this domain in gene-segment specific regulation. Our findings reveal a novel role for NP in selective regulation of viral gene segment replication and provide a framework for understanding how the expression patterns of individual viral gene segments can be modulated during adaptation to new host environments. IMPORTANCE Influenza A virus (IAV) is a respiratory pathogen that remains a significant source of morbidity and mortality. Escape from host immunity or emergence into new host species often requires mutations that modulate the functional activities of the viral glycoproteins hemagglutinin (HA) and neuraminidase (NA), which are responsible for virus attachment to and release from host cells, respectively. Maintaining the functional balance between the activities of HA and NA is required for fitness across multiple host systems. Thus, selective modulation of viral gene expression patterns may be a key determinant of viral immune escape and cross-species transmission potential. We identified a novel mechanism by which the viral nucleoprotein (NP) gene can selectively modulate NA segment replication and gene expression through interactions with the segment UTRs. Our work highlights an unexpected role for NP in selective regulation of expression from the individual IAV gene segments.
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Affiliation(s)
- Meghan Diefenbacher
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Timothy J. C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - David L. V. Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Beth M. Stadtmueller
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Nicholas C. Wu
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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12
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Fendler A, Shepherd STC, Au L, Wilkinson KA, Wu M, Schmitt AM, Tippu Z, Farag S, Rogiers A, Harvey R, Carlyle E, Edmonds K, Del Rosario L, Lingard K, Mangwende M, Holt L, Ahmod H, Korteweg J, Foley T, Barber T, Emslie-Henry A, Caulfield-Lynch N, Byrne F, Shum B, Gerard CL, Deng D, Kjaer S, Song OR, Queval C, Kavanagh C, Wall EC, Carr EJ, Namjou S, Caidan S, Gavrielides M, MacRae JI, Kelly G, Peat K, Kelly D, Murra A, Kelly K, O'Flaherty M, Shea RL, Gardner G, Murray D, Popat S, Yousaf N, Jhanji S, Van As N, Young K, Furness AJS, Pickering L, Beale R, Swanton C, Gandhi S, Gamblin S, Bauer DLV, Kassiotis G, Howell M, Nicholson E, Walker S, Wilkinson RJ, Larkin J, Turajlic S. Immune responses following third COVID-19 vaccination are reduced in patients with hematological malignancies compared to patients with solid cancer. Cancer Cell 2022; 40:438. [PMID: 35413273 PMCID: PMC8996376 DOI: 10.1016/j.ccell.2022.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Fendler A, Shepherd STC, Au L, Wu M, Harvey R, Schmitt AM, Tippu Z, Shum B, Farag S, Rogiers A, Carlyle E, Edmonds K, Del Rosario L, Lingard K, Mangwende M, Holt L, Ahmod H, Korteweg J, Foley T, Barber T, Emslie-Henry A, Caulfield-Lynch N, Byrne F, Deng D, Kjaer S, Song OR, Queval C, Kavanagh C, Wall EC, Carr EJ, Caidan S, Gavrielides M, MacRae JI, Kelly G, Peat K, Kelly D, Murra A, Kelly K, O'Flaherty M, Shea RL, Gardner G, Murray D, Yousaf N, Jhanji S, Tatham K, Cunningham D, Van As N, Young K, Furness AJS, Pickering L, Beale R, Swanton C, Gandhi S, Gamblin S, Bauer DLV, Kassiotis G, Howell M, Nicholson E, Walker S, Larkin J, Turajlic S. Omicron neutralising antibodies after third COVID-19 vaccine dose in patients with cancer. Lancet 2022; 399:905-907. [PMID: 35090602 PMCID: PMC8789238 DOI: 10.1016/s0140-6736(22)00147-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/15/2022] [Accepted: 01/23/2022] [Indexed: 12/16/2022]
Affiliation(s)
- Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Mary Wu
- High Throughput Screening Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Andreas M Schmitt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Zayd Tippu
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Benjamin Shum
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Sheima Farag
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Aljosja Rogiers
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Eleanor Carlyle
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Kim Edmonds
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Lyra Del Rosario
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Karla Lingard
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Mary Mangwende
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Lucy Holt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Hamid Ahmod
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Justine Korteweg
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Tara Foley
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Taja Barber
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | | | | | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Daqi Deng
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjaer
- Structural Biology Scientific Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Ok-Ryul Song
- High Throughput Screening Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Christophe Queval
- High Throughput Screening Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Caitlin Kavanagh
- High Throughput Screening Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Emma C Wall
- High Throughput Screening Laboratory, The Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust Biomedical Research Centre, London, UK
| | - Edward J Carr
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Simon Caidan
- Safety, Health & Sustainability, The Francis Crick Institute, London NW1 1AT, UK; University College London Cancer Institute, London, UK
| | - Mike Gavrielides
- Scientific Computing Scientific Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - James I MacRae
- Metabolomics Scientific Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Gavin Kelly
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, UK
| | - Kema Peat
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Denise Kelly
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Aida Murra
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Kayleigh Kelly
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Molly O'Flaherty
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Robyn L Shea
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London, UK; Translational Cancer Biochemistry Laboratory, Institute of Cancer Research, London, UK
| | - Gail Gardner
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Darren Murray
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Nadia Yousaf
- Lung Unit, The Royal Marsden NHS Foundation Trust, London, UK; Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London, UK
| | - Shaman Jhanji
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London, UK
| | - Kate Tatham
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London, UK
| | - David Cunningham
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Nicholas Van As
- Clincal Oncology Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Kate Young
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Andrew J S Furness
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Lisa Pickering
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Division of Medicine, University College London, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; UCL Queen Square Institute of Neurology, London, UK
| | - Steve Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - David L V Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Emma Nicholson
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Susanna Walker
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London, UK
| | - James Larkin
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK; Melanoma and Kidney Cancer Team, Institute of Cancer Research, London, UK.
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14
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Fendler A, Shepherd STC, Au L, Wilkinson KA, Wu M, Schmitt AM, Tippu Z, Farag S, Rogiers A, Harvey R, Carlyle E, Edmonds K, Del Rosario L, Lingard K, Mangwende M, Holt L, Ahmod H, Korteweg J, Foley T, Barber T, Emslie-Henry A, Caulfield-Lynch N, Byrne F, Shum B, Gerard CL, Deng D, Kjaer S, Song OR, Queval C, Kavanagh C, Wall EC, Carr EJ, Namjou S, Caidan S, Gavrielides M, MacRae JI, Kelly G, Peat K, Kelly D, Murra A, Kelly K, O'Flaherty M, Shea RL, Gardner G, Murray D, Yousaf N, Jhanji S, Van As N, Young K, Furness AJS, Pickering L, Beale R, Swanton C, Gandhi S, Gamblin S, Bauer DLV, Kassiotis G, Howell M, Nicholson E, Walker S, Wilkinson RJ, Larkin J, Turajlic S. Immune responses following third COVID-19 vaccination are reduced in patients with hematological malignancies compared to patients with solid cancer. Cancer Cell 2022; 40:114-116. [PMID: 34968417 PMCID: PMC8716090 DOI: 10.1016/j.ccell.2021.12.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Katalin A Wilkinson
- Tuberculosis Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Wellcome Center for Infectious Disease Research in Africa, University of Cape Town, Observatory 7925, Republic of South Africa
| | - Mary Wu
- High Throughput Screening Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Andreas M Schmitt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Zayd Tippu
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Sheima Farag
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Aljosja Rogiers
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London, NW1 1AT, UK
| | - Eleanor Carlyle
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Kim Edmonds
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Lyra Del Rosario
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Karla Lingard
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Mary Mangwende
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Lucy Holt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Hamid Ahmod
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Justine Korteweg
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Tara Foley
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Taja Barber
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Andrea Emslie-Henry
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | | | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Benjamin Shum
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Camille L Gerard
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Daqi Deng
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Svend Kjaer
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Ok-Ryul Song
- High Throughput Screening Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Christophe Queval
- High Throughput Screening Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Caitlin Kavanagh
- High Throughput Screening Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Emma C Wall
- Tuberculosis Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; University College London Hospitals NHS Foundation Trust Biomedical Research Centre, London, WC1E 6BT, UK
| | - Edward J Carr
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sina Namjou
- Safety, Health & Sustainability, The Francis Crick Institute, London, NW1 1AT, UK
| | - Simon Caidan
- Safety, Health & Sustainability, The Francis Crick Institute, London, NW1 1AT, UK
| | - Mike Gavrielides
- Scientific Computing Scientific Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - James I MacRae
- Metabolomics Scientific Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - Gavin Kelly
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Kema Peat
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Denise Kelly
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Aida Murra
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Kayleigh Kelly
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Molly O'Flaherty
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Robyn L Shea
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London, NW1 1AT, UK; Translational Cancer Biochemistry Laboratory, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Gail Gardner
- Translational Cancer Biochemistry Laboratory, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Darren Murray
- Translational Cancer Biochemistry Laboratory, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Nadia Yousaf
- Lung Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK; Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Shaman Jhanji
- Anaesthetics, Perioperative Medicine, and Pain Department, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Nicholas Van As
- Clincal Oncology Unit, The Royal Marsden NHS Foundation Trust, London, NW1 1AT, UK
| | - Kate Young
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Andrew J S Furness
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Lisa Pickering
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Rupert Beale
- University College London Hospitals NHS Foundation Trust Biomedical Research Centre, London, WC1E 6BT, UK; Division of Medicine, University College London, London NW1 2PG, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; University College London Cancer Institute, London WC1E 6DD, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Steve Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - David L V Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Emma Nicholson
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Susanna Walker
- Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Robert J Wilkinson
- Tuberculosis Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Wellcome Center for Infectious Disease Research in Africa, University of Cape Town, Observatory 7925, Republic of South Africa; Department of Infectious Disease, Imperial College London, London, W12 0NN, UK
| | - James Larkin
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK.
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Malinen AM, Bakermans J, Aalto-Setälä E, Blessing M, Bauer DLV, Parilova O, Belogurov GA, Dulin D, Kapanidis AN. Real-Time Single-Molecule Studies of RNA Polymerase-Promoter Open Complex Formation Reveal Substantial Heterogeneity Along the Promoter-Opening Pathway. J Mol Biol 2022; 434:167383. [PMID: 34863780 PMCID: PMC8783055 DOI: 10.1016/j.jmb.2021.167383] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 01/25/2023]
Abstract
The expression of most bacterial genes commences with the binding of RNA polymerase (RNAP)-σ70 holoenzyme to the promoter DNA. This initial RNAP-promoter closed complex undergoes a series of conformational changes, including the formation of a transcription bubble on the promoter and the loading of template DNA strand into the RNAP active site; these changes lead to the catalytically active open complex (RPO) state. Recent cryo-electron microscopy studies have provided detailed structural insight on the RPO and putative intermediates on its formation pathway. Here, we employ single-molecule fluorescence microscopy to interrogate the conformational dynamics and reaction kinetics during real-time RPO formation on a consensus lac promoter. We find that the promoter opening may proceed rapidly from the closed to open conformation in a single apparent step, or may instead involve a significant intermediate between these states. The formed RPO complexes are also different with respect to their transcription bubble stability. The RNAP cleft loops, and especially the β' rudder, stabilise the transcription bubble. The RNAP interactions with the promoter upstream sequence (beyond -35) stimulate transcription bubble nucleation and tune the reaction path towards stable forms of the RPO.
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Affiliation(s)
- Anssi M Malinen
- Department of Life Technologies, University of Turku, 20014 Turku, Finland; Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK.
| | - Jacob Bakermans
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Emil Aalto-Setälä
- Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Martin Blessing
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK; Max Planck Institute for the Science of Light, Staudtstraße 2, 91058 Erlangen, Germany
| | - David L V Bauer
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK; RNA Virus Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Olena Parilova
- Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | | | - David Dulin
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK; Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany; Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford.
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16
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Knight ML, Fan H, Bauer DLV, Grimes JM, Fodor E, Keown JR. Structure of an H3N2 influenza virus nucleoprotein. Acta Crystallogr F Struct Biol Commun 2021; 77:208-214. [PMID: 34196611 PMCID: PMC8248822 DOI: 10.1107/s2053230x2100635x] [Citation(s) in RCA: 8] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/18/2021] [Indexed: 11/10/2022] Open
Abstract
Influenza A viruses of the H1N1 and H3N2 subtypes are responsible for seasonal epidemic events. The influenza nucleoprotein (NP) binds to the viral genomic RNA and is essential for its replication. Efforts are under way to produce therapeutics and vaccines targeting the NP. Despite this, no structure of an NP from an H3N2 virus has previously been determined. Here, the structure of the A/Northern Territory/60/1968 (H3N2) influenza virus NP is presented at 2.2 Å resolution. The structure is highly similar to those of the A/WSN/1933 (H1N1) and A/Hong Kong/483/97 (H5N1) NPs. Nonconserved amino acids are widely dispersed both at the sequence and structural levels. A movement of the 73-90 RNA-binding loop is observed to be the key difference between the structure determined here and previous structures. The data presented here increase the understanding of structural conservation amongst influenza NPs and may aid in the design of universal interventions against influenza.
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Affiliation(s)
- Michael L. Knight
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - David L. V. Bauer
- RNA Virus Replication Laboratory, Francis Crick Institute, Midland Road, London NW1 1AT, United Kingdom
| | - Jonathan M. Grimes
- Division of Structural Biology, Welcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Jeremy R. Keown
- Division of Structural Biology, Welcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
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Bauer DLV, Tellier M, Martínez-Alonso M, Nojima T, Proudfoot NJ, Murphy S, Fodor E. Influenza Virus Mounts a Two-Pronged Attack on Host RNA Polymerase II Transcription. Cell Rep 2019; 23:2119-2129.e3. [PMID: 29768209 PMCID: PMC5972227 DOI: 10.1016/j.celrep.2018.04.047] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 04/03/2018] [Accepted: 04/11/2018] [Indexed: 12/24/2022] Open
Abstract
Influenza virus intimately associates with host RNA polymerase II (Pol II) and mRNA processing machinery. Here, we use mammalian native elongating transcript sequencing (mNET-seq) to examine Pol II behavior during viral infection. We show that influenza virus executes a two-pronged attack on host transcription. First, viral infection causes decreased Pol II gene occupancy downstream of transcription start sites. Second, virus-induced cellular stress leads to a catastrophic failure of Pol II termination at poly(A) sites, with transcription often continuing for tens of kilobases. Defective Pol II termination occurs independently of the ability of the viral NS1 protein to interfere with host mRNA processing. Instead, this termination defect is a common effect of diverse cellular stresses and underlies the production of previously reported downstream-of-gene transcripts (DoGs). Our work has implications for understanding not only host-virus interactions but also fundamental aspects of mammalian transcription. Influenza virus infection dysregulates host transcription Viral infection depletes Pol II from gene bodies downstream of the TSS Virus-induced stress leads to a catastrophic failure of Pol II termination Defective termination does not require viral NS1: host CPSF30 interaction
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Affiliation(s)
- David L V Bauer
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Mónica Martínez-Alonso
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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18
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Dadonaite B, Gilbertson B, Knight ML, Trifkovic S, Rockman S, Laederach A, Brown LE, Fodor E, Bauer DLV. The structure of the influenza A virus genome. Nat Microbiol 2019; 4:1781-1789. [PMID: 31332385 DOI: 10.1038/s41564-019-0513-7] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/12/2019] [Indexed: 12/19/2022]
Abstract
Influenza A viruses (IAVs) constitute a major threat to human health. The IAV genome consists of eight single-stranded viral RNA segments contained in separate viral ribonucleoprotein (vRNP) complexes that are packaged together into a single virus particle. The structure of viral RNA is believed to play a role in assembling the different vRNPs into budding virions1-8 and in directing reassortment between IAVs9. Reassortment between established human IAVs and IAVs harboured in the animal reservoir can lead to the emergence of pandemic influenza strains to which there is little pre-existing immunity in the human population10,11. While previous studies have revealed the overall organization of the proteins within vRNPs, characterization of viral RNA structure using conventional structural methods is hampered by limited resolution and an inability to resolve dynamic components12,13. Here, we employ multiple high-throughput sequencing approaches to generate a global high-resolution structure of the IAV genome. We show that different IAV genome segments acquire distinct RNA conformations and form both intra- and intersegment RNA interactions inside influenza virions. We use our detailed map of IAV genome structure to provide direct evidence for how intersegment RNA interactions drive vRNP cosegregation during reassortment between different IAV strains. The work presented here is a roadmap both for the development of improved vaccine strains and for the creation of a framework to 'risk assess' reassortment potential to better predict the emergence of new pandemic influenza strains.
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Affiliation(s)
| | - Brad Gilbertson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michael L Knight
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sanja Trifkovic
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Steven Rockman
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Seqirus Ltd, Parkville, Victoria, Australia
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Lorena E Brown
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| | - David L V Bauer
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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19
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Te Velthuis AJW, Long JC, Bauer DLV, Fan RLY, Yen HL, Sharps J, Siegers JY, Killip MJ, French H, Oliva-Martín MJ, Randall RE, de Wit E, van Riel D, Poon LLM, Fodor E. Mini viral RNAs act as innate immune agonists during influenza virus infection. Nat Microbiol 2018; 3:1234-1242. [PMID: 30224800 PMCID: PMC6203953 DOI: 10.1038/s41564-018-0240-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [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: 07/09/2018] [Accepted: 08/07/2018] [Indexed: 12/17/2022]
Abstract
The molecular processes that determine the outcome of influenza virus infection in humans are multifactorial and involve a complex interplay between host, viral and bacterial factors1. However, it is generally accepted that a strong innate immune dysregulation known as 'cytokine storm' contributes to the pathology of infections with the 1918 H1N1 pandemic or the highly pathogenic avian influenza viruses of the H5N1 subtype2-4. The RNA sensor retinoic acid-inducible gene I (RIG-I) plays an important role in sensing viral infection and initiating a signalling cascade that leads to interferon expression5. Here, we show that short aberrant RNAs (mini viral RNAs (mvRNAs)), produced by the viral RNA polymerase during the replication of the viral RNA genome, bind to and activate RIG-I and lead to the expression of interferon-β. We find that erroneous polymerase activity, dysregulation of viral RNA replication or the presence of avian-specific amino acids underlie mvRNA generation and cytokine expression in mammalian cells. By deep sequencing RNA samples from the lungs of ferrets infected with influenza viruses, we show that mvRNAs are generated during infection in vivo. We propose that mvRNAs act as the main agonists of RIG-I during influenza virus infection.
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Affiliation(s)
- Aartjan J W Te Velthuis
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
| | - Joshua C Long
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - David L V Bauer
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rebecca L Y Fan
- School of Public Health, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hui-Ling Yen
- School of Public Health, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Jane Sharps
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jurre Y Siegers
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Marian J Killip
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Biomedical Sciences Research Complex, North Haugh, University of St Andrews, St Andrews, UK
| | - Hollie French
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | | | - Richard E Randall
- Biomedical Sciences Research Complex, North Haugh, University of St Andrews, St Andrews, UK
| | - Emmie de Wit
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Debby van Riel
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Leo L M Poon
- School of Public Health, University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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20
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Dulin D, Bauer DLV, Malinen AM, Bakermans JJW, Kaller M, Morichaud Z, Petushkov I, Depken M, Brodolin K, Kulbachinskiy A, Kapanidis AN. Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria. Nat Commun 2018; 9:1478. [PMID: 29662062 PMCID: PMC5902446 DOI: 10.1038/s41467-018-03902-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [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: 06/17/2017] [Accepted: 03/20/2018] [Indexed: 01/25/2023] Open
Abstract
Transcription in bacteria is controlled by multiple molecular mechanisms that precisely regulate gene expression. It has been recently shown that initial RNA synthesis by the bacterial RNA polymerase (RNAP) is interrupted by pauses; however, the pausing determinants and the relationship of pausing with productive and abortive RNA synthesis remain poorly understood. Using single-molecule FRET and biochemical analysis, here we show that the pause encountered by RNAP after the synthesis of a 6-nt RNA (ITC6) renders the promoter escape strongly dependent on the NTP concentration. Mechanistically, the paused ITC6 acts as a checkpoint that directs RNAP to one of three competing pathways: productive transcription, abortive RNA release, or a new unscrunching/scrunching pathway. The cyclic unscrunching/scrunching of the promoter generates a long-lived, RNA-bound paused state; the abortive RNA release and DNA unscrunching are thus not as tightly linked as previously thought. Finally, our new model couples the pausing with the abortive and productive outcomes of initial transcription.
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Affiliation(s)
- David Dulin
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK.
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Hartmannstrasse 14, 91052, Erlangen, Germany.
| | - David L V Bauer
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Anssi M Malinen
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
- Department of Biochemistry, University of Turku, 20014, Turku, Finland
| | - Jacob J W Bakermans
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Martin Kaller
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Zakia Morichaud
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR9004 CNRS-Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, France
| | - Ivan Petushkov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Konstantin Brodolin
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR9004 CNRS-Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, France
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK.
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21
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Eaton JD, Davidson L, Bauer DLV, Natsume T, Kanemaki MT, West S. Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity. Genes Dev 2018; 32:127-139. [PMID: 29432121 PMCID: PMC5830926 DOI: 10.1101/gad.308528.117] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [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: 10/23/2017] [Accepted: 01/05/2018] [Indexed: 12/31/2022]
Abstract
In this study, Eaton et al. use a new gene-editing approach to delineate the mechanism by which RNA polymerase II terminates. They generated human cell lines from which the 5′-to-3′ exoribonuclease Xrn2 or the poly(A) signal endoribonuclease CPSF73 can be rapidly controlled and show that efficient termination on most protein-coding genes involves CPSF73-mediated RNA cleavage and cotranscriptional degradation of polymerase-associated RNA by Xrn2. Termination is a ubiquitous phase in every transcription cycle but is incompletely understood and a subject of debate. We used gene editing as a new approach to address its mechanism through engineered conditional depletion of the 5′ → 3′ exonuclease Xrn2 or the polyadenylation signal (PAS) endonuclease CPSF73 (cleavage and polyadenylation specificity factor 73). The ability to rapidly control Xrn2 reveals a clear and general role for it in cotranscriptional degradation of 3′ flanking region RNA and transcriptional termination. This defect is characterized genome-wide at high resolution using mammalian native elongating transcript sequencing (mNET-seq). An Xrn2 effect on termination requires prior RNA cleavage, and we provide evidence for this by showing that catalytically inactive CPSF73 cannot restore termination to cells lacking functional CPSF73. Notably, Xrn2 plays no significant role in either Histone or small nuclear RNA (snRNA) gene termination even though both RNA classes undergo 3′ end cleavage. In sum, efficient termination on most protein-coding genes involves CPSF73-mediated RNA cleavage and cotranscriptional degradation of polymerase-associated RNA by Xrn2. However, as CPSF73 loss caused more extensive readthrough transcription than Xrn2 elimination, it likely plays a more underpinning role in termination.
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Affiliation(s)
- Joshua D Eaton
- The Living Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Lee Davidson
- The Living Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom.,Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - David L V Bauer
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Toyoaki Natsume
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan
| | - Steven West
- The Living Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
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22
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Duchi D, Bauer DLV, Fernandez L, Evans G, Robb N, Hwang LC, Gryte K, Tomescu A, Zawadzki P, Morichaud Z, Brodolin K, Kapanidis AN. RNA Polymerase Pausing during Initial Transcription. Mol Cell 2016; 63:939-50. [PMID: 27618490 PMCID: PMC5031556 DOI: 10.1016/j.molcel.2016.08.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [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: 05/22/2015] [Revised: 04/12/2016] [Accepted: 08/05/2016] [Indexed: 11/11/2022]
Abstract
In bacteria, RNA polymerase (RNAP) initiates transcription by synthesizing short transcripts that are either released or extended to allow RNAP to escape from the promoter. The mechanism of initial transcription is unclear due to the presence of transient intermediates and molecular heterogeneity. Here, we studied initial transcription on a lac promoter using single-molecule fluorescence observations of DNA scrunching on immobilized transcription complexes. Our work revealed a long pause (“initiation pause,” ∼20 s) after synthesis of a 6-mer RNA; such pauses can serve as regulatory checkpoints. Region sigma 3.2, which contains a loop blocking the RNA exit channel, was a major pausing determinant. We also obtained evidence for RNA backtracking during abortive initial transcription and for additional pausing prior to escape. We summarized our work in a model for initial transcription, in which pausing is controlled by a complex set of determinants that modulate the transition from a 6- to a 7-nt RNA. E. coli RNA polymerase pauses during initial transcription at lac promoters Initiation pausing lasts for ∼20 s and occurs at the transition from 6- to 7-nt RNA Region 3.2 of σ70 is the main protein element controlling pausing Pausing is likely to be controlled further by a complex set of determinants
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Affiliation(s)
- Diego Duchi
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - David L V Bauer
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Laurent Fernandez
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Geraint Evans
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Nicole Robb
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Ling Chin Hwang
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Kristofer Gryte
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Alexandra Tomescu
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Pawel Zawadzki
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Zakia Morichaud
- CNRS FRE 3689, Centre d'études d'agents Pathogénes et Biotechnologies pour la Santé (CPBS), 1919 route de Mende, 34293 Montpellier, France
| | - Konstantin Brodolin
- CNRS FRE 3689, Centre d'études d'agents Pathogénes et Biotechnologies pour la Santé (CPBS), 1919 route de Mende, 34293 Montpellier, France
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK.
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23
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Abstract
Mitotic chromosome structure is pivotal to cell division but difficult to observe in fine detail using conventional methods. DNA catenation has been implicated in both sister chromatid cohesion and chromosome condensation, but has never been observed directly. We have used a lab-on-a-chip microfluidic device and fluorescence microscopy, coupled with a simple image analysis pipeline, to digest chromosomal proteins and examine the structure of the remaining DNA, which maintains the canonical 'X' shape. By directly staining DNA, we observe that DNA catenation between sister chromatids (separated by fluid flow) is composed of distinct fibres of DNA concentrated at the centromeres. Disrupting the catenation of the chromosomes with Topoisomerase IIα significantly alters overall chromosome shape, suggesting that DNA catenation must be simultaneously maintained for correct chromosome condensation, and destroyed to complete sister chromatid disjunction. In addition to demonstrating the value of microfluidics as a tool for examining chromosome structure, these results lend support to certain models of DNA catenation organization and regulation: in particular, we conclude from our observation of centromere-concentrated catenation that spindle forces could play a driving role in decatenation and that Topoisomerase IIα is differentially regulated at the centromeres, perhaps in conjunction with cohesin.
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Affiliation(s)
- David L V Bauer
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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24
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Yusuf M, Bauer DLV, Lipinski DM, MacLaren RE, Wade-Martins R, Mir KU, Volpi EV. Combining M-FISH and Quantum Dot technology for fast chromosomal assignment of transgenic insertions. BMC Biotechnol 2011; 11:121. [PMID: 22165957 PMCID: PMC3266222 DOI: 10.1186/1472-6750-11-121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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: 10/06/2011] [Accepted: 12/13/2011] [Indexed: 12/01/2022] Open
Abstract
Background Physical mapping of transgenic insertions by Fluorescence in situ Hybridization (FISH) is a reliable and cost-effective technique. Chromosomal assignment is commonly achieved either by concurrent G-banding or by a multi-color FISH approach consisting of iteratively co-hybridizing the transgenic sequence of interest with one or more chromosome-specific probes at a time, until the location of the transgenic insertion is identified. Results Here we report a technical development for fast chromosomal assignment of transgenic insertions at the single cell level in mouse and rat models. This comprises a simplified 'single denaturation mixed hybridization' procedure that combines multi-color karyotyping by Multiplex FISH (M-FISH), for simultaneous and unambiguous identification of all chromosomes at once, and the use of a Quantum Dot (QD) conjugate for the transgene detection. Conclusions Although the exploitation of the unique optical properties of QD nanocrystals, such as photo-stability and brightness, to improve FISH performance generally has been previously investigated, to our knowledge this is the first report of a purpose-designed molecular cytogenetic protocol in which the combined use of QDs and standard organic fluorophores is specifically tailored to assist gene transfer technology.
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Affiliation(s)
- Mohammed Yusuf
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
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