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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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Martin SB, Polubothu S, Bruzos AL, Kelly G, Horswell S, Sauvadet A, Bryant D, Zecchin D, Riachi M, Michailidis F, Sadri A, Muwanga-Nanyonjo N, Lopez-Balboa P, Knöpfel N, Bulstrode N, Pittman A, Yeh I, Kinsler VA. Mosaic BRAF Fusions Are a Recurrent Cause of Congenital Melanocytic Nevi Targetable by MAPK Pathway Inhibition. J Invest Dermatol 2024; 144:593-600.e7. [PMID: 37716647 DOI: 10.1016/j.jid.2023.06.213] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 09/18/2023]
Abstract
Among children with multiple congenital melanocytic nevi, 25% have no established genetic cause, of whom many develop a hyperproliferative and severely pruritic phenotype resistant to treatment. Gene fusions have been reported in individual cases of congenital melanocytic nevi. We studied 169 patients with congenital melanocytic nevi in this study, 38 of whom were double wild type for pathogenic NRAS/BRAF variants. Nineteen of these 38 patients had sufficient tissue to undergo RNA sequencing, which revealed mosaic BRAF fusions in 11 of 19 patients and mosaic RAF1 fusions in 1 of 19. Recurrently, fusions involved the loss of the 5´ regulatory domain of BRAF or RAF1 but preserved the kinase domain. We validated all cases and detected the fusions in two separate nevi in 5 of 12 patients, confirming clonality. The absence of the fusion in blood in 8 of 12 patients indicated mosaicism. Primary culture of BRAF-fusion nevus cells from 3 of 12 patients demonstrated highly increased MAPK activation, despite only mildly increased BRAF expression, suggesting additional mechanisms of kinase activation. Trametinib quenched MAPK hyperactivation in vitro, and treatment of two patients caused rapid improvement in bulk tissue, improving bodily movement and reducing inflammation and severe pruritus. These findings offer a genetic diagnosis to an additional group of patients and trametinib as a treatment option for the severe associated phenotypes.
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Affiliation(s)
- Sara Barberan Martin
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Satyamaanasa Polubothu
- Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom; Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Alicia Lopez Bruzos
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Gavin Kelly
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, United Kingdom
| | - Stuart Horswell
- Open Targets, Welcome Sanger Institute, Cambridge, United Kingdom
| | - Aimie Sauvadet
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Dale Bryant
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Davide Zecchin
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Melissa Riachi
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Fanourios Michailidis
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Amir Sadri
- Plastic and Reconstructive Surgery, Great Ormond Street Hospital for Children and UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Noreen Muwanga-Nanyonjo
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom
| | - Pablo Lopez-Balboa
- Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Nicole Knöpfel
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom; Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Neil Bulstrode
- Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Alan Pittman
- Genetics Research Centre (A.P.), St George's University of London, London, United Kingdom
| | - Iwei Yeh
- Dermatology and Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Veronica A Kinsler
- Mosaicism and Precision Medicine laboratory, The Francis Crick Institute, London, United Kingdom; Genetics and Genomic Medicine, UCL Great Osmond Street Institute of Child Health, London, United Kingdom; Paediatric Dermatology, Great Ormond Street Hospital for Children, London, United Kingdom.
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3
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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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4
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Ziff OJ, Harley J, Wang Y, Neeves J, Tyzack G, Ibrahim F, Skehel M, Chakrabarti AM, Kelly G, Patani R. Nucleocytoplasmic mRNA redistribution accompanies RNA binding protein mislocalization in ALS motor neurons and is restored by VCP ATPase inhibition. Neuron 2023; 111:3011-3027.e7. [PMID: 37480846 DOI: 10.1016/j.neuron.2023.06.019] [Citation(s) in RCA: 1] [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: 10/19/2022] [Revised: 05/09/2023] [Accepted: 06/22/2023] [Indexed: 07/24/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by nucleocytoplasmic mislocalization of the RNA-binding protein (RBP) TDP-43. However, emerging evidence suggests more widespread mRNA and protein mislocalization. Here, we employed nucleocytoplasmic fractionation, RNA sequencing, and mass spectrometry to investigate the localization of mRNA and protein in induced pluripotent stem cell-derived motor neurons (iPSMNs) from ALS patients with TARDBP and VCP mutations. ALS mutant iPSMNs exhibited extensive nucleocytoplasmic mRNA redistribution, RBP mislocalization, and splicing alterations. Mislocalized proteins exhibited a greater affinity for redistributed transcripts, suggesting a link between RBP mislocalization and mRNA redistribution. Notably, treatment with ML240, a VCP ATPase inhibitor, partially restored mRNA and protein localization in ALS mutant iPSMNs. ML240 induced changes in the VCP interactome and lysosomal localization and reduced oxidative stress and DNA damage. These findings emphasize the link between RBP mislocalization and mRNA redistribution in ALS motor neurons and highlight the therapeutic potential of VCP inhibition.
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Affiliation(s)
- Oliver J Ziff
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK; National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, WC1N 3BG London, UK.
| | - Jasmine Harley
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK; Institute of Molecular and Cell Biology, A(∗)STAR Research Entities, Singapore 138673, Singapore
| | - Yiran Wang
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Jacob Neeves
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Giulia Tyzack
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Fairouz Ibrahim
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Mark Skehel
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | | | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK; National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, WC1N 3BG London, UK.
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5
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Townsend L, Kelly G, Kenny C, McGrath J, Donohue S, Allen N, Doherty L, Noonan N, Martin G, Fleming C, Bergin C. Healthcare Worker Characteristics Associated with SARS-CoV-2 Vaccine Uptake in Ireland; a Multicentre Cross-Sectional Study. Vaccines (Basel) 2023; 11:1529. [PMID: 37896933 PMCID: PMC10610998 DOI: 10.3390/vaccines11101529] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The prevention of SARS-CoV-2 acquisition and transmission among healthcare workers is an ongoing challenge. Vaccination has been introduced to mitigate these risks. Vaccine uptake varies among healthcare workers in the absence of vaccine mandates. We investigated engagement with SARS-CoV-2 vaccination among healthcare workers and identified characteristics associated with lower vaccine uptake. This multi-site cross-sectional study recruited n = 1260 healthcare workers in both clinical and non-clinical roles over a three-month period from November 2022. Participants reported their engagement with the primary SARS-CoV-2 vaccination programme and subsequent booster programmes, as well as providing demographic, occupational and personal medical history information. Multivariable linear regression identified characteristics associated with vaccine uptake. Engagement with vaccination programmes was high, with 88% of participants receiving at least one booster dose after primary vaccination course. Younger age and female sex were associated with reduced vaccine uptake. Healthcare workers in non-clinical roles also had reduced vaccine uptake. These findings should inform vaccination strategies across healthcare settings and target populations with reduced vaccine uptake directly, in particular young, female, and non-clinical healthcare workers, both for SARS-CoV-2 and other healthcare-associated vaccine-preventable infections.
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Affiliation(s)
- Liam Townsend
- Department of Infectious Diseases, St James’s Hospital, D08 NHY1 Dublin, Ireland; (L.T.)
| | - Gavin Kelly
- Department of Infectious Diseases, University Hospital Galway, H91 YR71 Galway, Ireland
| | - Claire Kenny
- Department of Infectious Diseases, University Hospital Galway, H91 YR71 Galway, Ireland
| | - Jonathan McGrath
- Department of Infectious Diseases, St James’s Hospital, D08 NHY1 Dublin, Ireland; (L.T.)
| | - Seán Donohue
- Department of Infectious Diseases, St James’s Hospital, D08 NHY1 Dublin, Ireland; (L.T.)
| | - Niamh Allen
- Department of Infectious Diseases, St James’s Hospital, D08 NHY1 Dublin, Ireland; (L.T.)
| | | | - Noirin Noonan
- Department of Occupational Medicine, St James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Greg Martin
- Health Protection Surveillance Centre, D01 A4A3 Dublin, Ireland
| | | | - Catherine Fleming
- Department of Infectious Diseases, University Hospital Galway, H91 YR71 Galway, Ireland
| | - Colm Bergin
- Department of Infectious Diseases, St James’s Hospital, D08 NHY1 Dublin, Ireland; (L.T.)
- Department of Clinical Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland
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6
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Carr EJ, Wu MY, Gahir J, Harvey R, Townsley H, Bailey C, Fowler AS, Dowgier G, Hobbs A, Herman L, Ragno M, Miah M, Bawumia P, Smith C, Miranda M, Mears HV, Adams L, Haptipoglu E, O'Reilly N, Warchal S, Sawyer C, Ambrose K, Kelly G, Beale R, Papineni P, Corrah T, Gilson R, Gamblin S, Kassiotis G, Libri V, Williams B, Swanton C, Gandhi S, Lv Bauer D, Wall EC. Neutralising immunity to omicron sublineages BQ.1.1, XBB, and XBB.1.5 in healthy adults is boosted by bivalent BA.1-containing mRNA vaccination and previous Omicron infection. Lancet Infect Dis 2023:S1473-3099(23)00289-X. [PMID: 37290472 DOI: 10.1016/s1473-3099(23)00289-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 06/10/2023]
Affiliation(s)
- Edward J Carr
- The Francis Crick Institute, London, UK; University College London, London, UK
| | - Mary Y Wu
- COVID Surveillance Unit, London, UK; The Francis Crick Institute, London, UK
| | - Joshua Gahir
- The Francis Crick Institute, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | | | - Hermaleigh Townsley
- The Francis Crick Institute, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | - Chris Bailey
- The Francis Crick Institute, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | | | | | | | | | | | | | | | | | | | | | | | - Emine Haptipoglu
- The Francis Crick Institute, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | | | | | | | | | | | - Rupert Beale
- The Francis Crick Institute, London, UK; University College London, London, UK
| | | | - Tumena Corrah
- London Northwest University Healthcare NHS Trust, London, UK
| | - Richard Gilson
- Central and North West London NHS Foundation Trust, London, UK
| | | | - George Kassiotis
- The Francis Crick Institute, London, UK; Department of Infectious Disease, St Mary's Hospital, Imperial College London, London, UK
| | - Vincenzo Libri
- University College London, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | - Bryan Williams
- University College London, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | - Charles Swanton
- The Francis Crick Institute, London, UK; University College London, London, UK
| | - Sonia Gandhi
- The Francis Crick Institute, London, UK; University College London, London, UK
| | | | - Emma C Wall
- The Francis Crick Institute, London, UK; University College London, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK.
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7
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Allworth MB, Goonan B, Nelson JE, Kelly G, McGrath SR, Woodgate RG. Comparison of the efficacy of macrocyclic lactone anthelmintics, either singly or in combination with other anthelmintic(s), in nine beef herds in southern NSW. Aust Vet J 2023. [PMID: 37158491 DOI: 10.1111/avj.13248] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 03/26/2023] [Accepted: 04/09/2023] [Indexed: 05/10/2023]
Abstract
Anthelmintic resistance (AR) is a well-recognized challenge in farmed ruminants. The use of anthelmintics in combination is one of the strategies recommended to slow the rate of AR development. Two studies were undertaken in 2017 and 2019 to assess the efficacy of single-dose macrocyclic lactone (ML) anthelmintic and ML combination drenches. In total, 11 Faecal Egg Count Reduction Trials (FECRTs) were set up in 10 different beef herds, with results available from 10 of those FECRTs (9 herds). AR to a single ML anthelmintic was detected in all 9 herds, with resistance to Cooperia and Haemonchus spp on 9 farms, and resistance to Ostertagia and Trichostrongylus spp on 2 farms. In contrast, for the ML combination anthelmintics, all FECRTs resulted in efficacies of 99%-100%. The results suggest that cattle producers should strongly consider using combination drenches in their herds in preference to single actives.
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Affiliation(s)
- M B Allworth
- Fred Morley Centre, Charles Sturt University, Wagga Wagga, New South Wales, 2678, Australia
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, 2678, Australia
- Gulbali institute, Charles Sturt University, Wagga Wagga, New South Wales, 2678, Australia
| | - B Goonan
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, 2678, Australia
| | - J E Nelson
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, 2678, Australia
| | - G Kelly
- Boehringer Ingelheim Animal Health Australia Pty. Ltd., Macquarie Park, New South Wales, Australia
| | - S R McGrath
- Fred Morley Centre, Charles Sturt University, Wagga Wagga, New South Wales, 2678, Australia
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, 2678, Australia
- Gulbali institute, Charles Sturt University, Wagga Wagga, New South Wales, 2678, Australia
| | - R G Woodgate
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, 2678, Australia
- Gulbali institute, Charles Sturt University, Wagga Wagga, New South Wales, 2678, Australia
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8
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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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9
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Ziff OJ, Neeves J, Mitchell J, Tyzack G, Martinez-Ruiz C, Luisier R, Chakrabarti AM, McGranahan N, Litchfield K, Boulton SJ, Al-Chalabi A, Kelly G, Humphrey J, Patani R. Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology. Nat Commun 2023; 14:2176. [PMID: 37080969 PMCID: PMC10119258 DOI: 10.1038/s41467-023-37630-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 09/09/2022] [Accepted: 03/22/2023] [Indexed: 04/22/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) causes motor neuron degeneration, with 97% of cases exhibiting TDP-43 proteinopathy. Elucidating pathomechanisms has been hampered by disease heterogeneity and difficulties accessing motor neurons. Human induced pluripotent stem cell-derived motor neurons (iPSMNs) offer a solution; however, studies have typically been limited to underpowered cohorts. Here, we present a comprehensive compendium of 429 iPSMNs from 15 datasets, and 271 post-mortem spinal cord samples. Using reproducible bioinformatic workflows, we identify robust upregulation of p53 signalling in ALS in both iPSMNs and post-mortem spinal cord. p53 activation is greatest with C9orf72 repeat expansions but is weakest with SOD1 and FUS mutations. TDP-43 depletion potentiates p53 activation in both post-mortem neuronal nuclei and cell culture, thereby functionally linking p53 activation with TDP-43 depletion. ALS iPSMNs and post-mortem tissue display enrichment of splicing alterations, somatic mutations, and gene fusions, possibly contributing to the DNA damage response.
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Affiliation(s)
- Oliver J Ziff
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
- National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK.
| | - Jacob Neeves
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jamie Mitchell
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Giulia Tyzack
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Carlos Martinez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Raphaelle Luisier
- Genomics and Health Informatics Group, Idiap Research Institute, Martigny, Switzerland
| | | | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
- National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK.
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10
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Zani F, Blagih J, Gruber T, Buck MD, Jones N, Hennequart M, Newell CL, Pilley SE, Soro-Barrio P, Kelly G, Legrave NM, Cheung EC, Gilmore IS, Gould AP, Garcia-Caceres C, Vousden KH. The dietary sweetener sucralose is a negative modulator of T cell-mediated responses. Nature 2023; 615:705-711. [PMID: 36922598 PMCID: PMC10033444 DOI: 10.1038/s41586-023-05801-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/06/2023] [Indexed: 03/17/2023]
Abstract
Artificial sweeteners are used as calorie-free sugar substitutes in many food products and their consumption has increased substantially over the past years1. Although generally regarded as safe, some concerns have been raised about the long-term safety of the consumption of certain sweeteners2-5. In this study, we show that the intake of high doses of sucralose in mice results in immunomodulatory effects by limiting T cell proliferation and T cell differentiation. Mechanistically, sucralose affects the membrane order of T cells, accompanied by a reduced efficiency of T cell receptor signalling and intracellular calcium mobilization. Mice given sucralose show decreased CD8+ T cell antigen-specific responses in subcutaneous cancer models and bacterial infection models, and reduced T cell function in models of T cell-mediated autoimmunity. Overall, these findings suggest that a high intake of sucralose can dampen T cell-mediated responses, an effect that could be used in therapy to mitigate T cell-dependent autoimmune disorders.
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Affiliation(s)
- Fabio Zani
- p53 and Metabolism Laboratory, The Francis Crick Institute, London, UK.
| | - Julianna Blagih
- p53 and Metabolism Laboratory, The Francis Crick Institute, London, UK.
- University of Montreal, Maisonneuve-Rosemont Hospital Research Centre, Montreal, Quebec, Canada.
| | - Tim Gruber
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München and German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Michael D Buck
- Immunobiology Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas Jones
- Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, UK
| | - Marc Hennequart
- p53 and Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Clare L Newell
- National Physical Laboratory, Teddington, UK
- Laboratory of Physiology and Metabolism, The Francis Crick Institute, London, UK
| | - Steven E Pilley
- p53 and Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Pablo Soro-Barrio
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Nathalie M Legrave
- Metabolomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Eric C Cheung
- p53 and Metabolism Laboratory, The Francis Crick Institute, London, UK
| | | | - Alex P Gould
- Laboratory of Physiology and Metabolism, The Francis Crick Institute, London, UK
| | - Cristina Garcia-Caceres
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München and German Center for Diabetes Research (DZD), Neuherberg, Germany
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Karen H Vousden
- p53 and Metabolism Laboratory, The Francis Crick Institute, London, UK.
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11
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Natalini A, Simonetti S, Favaretto G, Lucantonio L, Peruzzi G, Muñoz-Ruiz M, Kelly G, Contino AM, Sbrocchi R, Battella S, Capone S, Folgori A, Nicosia A, Santoni A, Hayday AC, Di Rosa F. Corrigendum: Improved memory CD8 T cell response to delayed vaccine boost is associated with a distinct molecular signature. Front Immunol 2023; 14:1199754. [PMID: 37205109 PMCID: PMC10188117 DOI: 10.3389/fimmu.2023.1199754] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 04/07/2023] [Indexed: 05/21/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fimmu.2023.1043631.].
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Affiliation(s)
- Ambra Natalini
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
- *Correspondence: Ambra Natalini, ; Francesca Di Rosa,
| | - Sonia Simonetti
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
| | - Gabriele Favaretto
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
| | - Lorenzo Lucantonio
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
- Department of Molecular Medicine, University of Rome “Sapienza”, Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Miguel Muñoz-Ruiz
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Gavin Kelly
- Bioinformatic and Biostatistics Science and Technology Platform, The Francis Crick Institute, London, United Kingdom
| | | | | | | | | | | | - Alfredo Nicosia
- CEINGE, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | - Adrian C. Hayday
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom
- Peter Gorer Department of Immunobiology, King’s College London, London, United Kingdom
- National Institute for Health Research (NIHR), Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Francesca Di Rosa
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
- *Correspondence: Ambra Natalini, ; Francesca Di Rosa,
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12
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Natalini A, Simonetti S, Favaretto G, Lucantonio L, Peruzzi G, Muñoz-Ruiz M, Kelly G, Contino AM, Sbrocchi R, Battella S, Capone S, Folgori A, Nicosia A, Santoni A, Hayday AC, Di Rosa F. Improved memory CD8 T cell response to delayed vaccine boost is associated with a distinct molecular signature. Front Immunol 2023; 14:1043631. [PMID: 36865556 PMCID: PMC9973452 DOI: 10.3389/fimmu.2023.1043631] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/09/2023] [Indexed: 02/16/2023] Open
Abstract
Effective secondary response to antigen is a hallmark of immunological memory. However, the extent of memory CD8 T cell response to secondary boost varies at different times after a primary response. Considering the central role of memory CD8 T cells in long-lived protection against viral infections and tumors, a better understanding of the molecular mechanisms underlying the changing responsiveness of these cells to antigenic challenge would be beneficial. We examined here primed CD8 T cell response to boost in a BALB/c mouse model of intramuscular vaccination by priming with HIV-1 gag-encoding Chimpanzee adenovector, and boosting with HIV-1 gag-encoding Modified Vaccinia virus Ankara. We found that boost was more effective at day(d)100 than at d30 post-prime, as evaluated at d45 post-boost by multi-lymphoid organ assessment of gag-specific CD8 T cell frequency, CD62L-expression (as a guide to memory status) and in vivo killing. RNA-sequencing of splenic gag-primed CD8 T cells at d100 revealed a quiescent, but highly responsive signature, that trended toward a central memory (CD62L+) phenotype. Interestingly, gag-specific CD8 T cell frequency selectively diminished in the blood at d100, relative to the spleen, lymph nodes and bone marrow. These results open the possibility to modify prime/boost intervals to achieve an improved memory CD8 T cell secondary response.
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Affiliation(s)
- Ambra Natalini
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
| | - Sonia Simonetti
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
| | - Gabriele Favaretto
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
| | - Lorenzo Lucantonio
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy.,Department of Molecular Medicine, University of Rome "Sapienza", Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Miguel Muñoz-Ruiz
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Gavin Kelly
- Bioinformatic and Biostatistics Science and Technology Platform, The Francis Crick Institute, London, United Kingdom
| | | | | | | | | | | | - Alfredo Nicosia
- CEINGE, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | - Adrian C Hayday
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom.,Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom.,National Institute for Health Research (NIHR), Biomedical Research Center (BRC), Guy's and St Thomas' NHS Foundation Trust and King's College London, London, United Kingdom
| | - Francesca Di Rosa
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
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13
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Martin SB, Polubothu S, Bruzos A, Lopez-Balboa P, Bulstrode N, Kelly G, Kinsler V. 260 Mosaic BRAF fusions are a recurrent cause of multiple congenital melanocytic naevi. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.09.272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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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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Storm K, Kelly G, Kottapalli A, Kaissieh D, Osio V, Zoorob D. Published Support for Wellness, Diversity, Equity, and Inclusion Among Internal Medicine Residency Program Websites. Cureus 2022; 14:e29328. [PMID: 36277535 PMCID: PMC9580599 DOI: 10.7759/cureus.29328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2022] [Indexed: 11/05/2022] Open
Abstract
Introduction: The objective of this study was to review internal medicine residency program websites in the United States based on their published support for wellness, diversity, equity, and inclusion concepts. Inclusion of wellness, diversity, equity, and inclusion on program websites can serve as critical student benchmarks, and it may be paramount to optimize residency program websites accordingly. Methods: This is a cross-sectional study of the websites of 597 internal medicine residency programs accredited by the Accreditation Council for Graduate Medical Education between March 25 and April 25, 2022. The websites were assessed based on 22 characteristics consisting of wellness verbiage, gender and underrepresented in medicine evaluation of faculty and residents, and diversity, equity, and inclusion-related semantics. Website photos were used to assess ethnic/sex representation. These attributes were devised by two sequentially set up focus groups consisting of 49 racially, ethnically, and gender-diverse medical students. Results: A total of 579 internal medicine programs were reviewed. Only 239 (41%) had a dedicated page for resident wellness activities and efforts, while 134 (19%) had no mention of the concept throughout their web pages. Similarly, only 136 (23%) had a dedicated wellness officer, whether faculty or resident, who was focused on departmental interests. Gender diversity could be determined in 445 (77%) and 459 (79%) websites for faculty and residents, respectively. Underrepresented in medicine faculty and residents was noted in 293 (51%) and 393 (68%) of websites, respectively. A diversity, equity, and inclusion section was present in 172 (30%) of programs, with 93 (16%) having an assigned faculty or resident. Chairpersons or program directors stressed diversity, equity, and inclusion in up to 456 (79%) of the websites, with 181 (31%) having program mission statements or goals that include diversity, equity, and inclusion verbiage. Conclusion: A deficit of various essential wellness, diversity, equity, and inclusion attributes persists across internal medicine residency websites. Residency programs would benefit from optimizing their websites to attract more diverse applicants.
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16
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Naito Y, Hynds R, Novo D, Chakravarty P, Kelly G, Swanton C, Honda K, Sahai E. Abstract 674: Tracking the transcriptome of lung cancer-associated fibroblasts within the TRACERx lung study from patient to culture models reveals phenotypic plasticity and instructive cues from cancer cells. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer-associated fibroblasts (CAFs) play a pivotal role in cancer progression by enhancing extracellular matrix remodeling, cancer cell invasion, and mediating inflammatory environment. Therefore, CAFs have become targets for cancer therapies. However, a major hurdle to developing such therapies are the challenges of studying CAFs in culture - specifically it remains unclear which CAF functions and phenotypes are sustained during in vitro culture and the signaling pathways driving distinct CAF phenotypes.
We investigated whether CAF phenotypes and functions are sustained or changed during 2D CAF culture under in vitro systems, our analysis included early passage, late passage, and immortalized cultures, as well as CAFs in coculture with cancer cell lines. Transcriptomic analysis revealed that inflammatory-related gene expression programs were suppressed in late passage and immortalized CAFs compared with early passage equivalents. Direct co-culture with lung cancer cells can revert the inflammatory gene expressions in immortalized CAFs such that they partially resemble early passage CAFs. In contrast, indirect coculture with lung cancer cells - in which CAFs could not form cell-cell contacts with cancer cells - had a less significant effect on immortalized CAF inflammatory gene expression but could induce TGFβ regulated genes. Interestingly, inhibition of the TGFβ signaling pathway potentiated the inflammatory gene expression network induced by direct co-culture, suggesting that the signaling mediated by direct cellular interaction is antagonistic to the TGFβ signaling pathway.
These data further our understanding of cancer cell – CAF crosstalk and will help to develop in vitro assays that more closely maintain the state of CAFs observed in tissue.
Citation Format: Yutaka Naito, Robert Hynds, David Novo, Probir Chakravarty, Gavin Kelly, Charles Swanton, Kazufumi Honda, Erik Sahai, TRACERx Consortium. Tracking the transcriptome of lung cancer-associated fibroblasts within the TRACERx lung study from patient to culture models reveals phenotypic plasticity and instructive cues from cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 674.
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Affiliation(s)
- Yutaka Naito
- 1Institute for Advanced Medical Sciences, Nippon Medical University, Tokyo, Japan
| | - Robert Hynds
- 2University College London Cancer Institute, University College London, London, United Kingdom
| | - David Novo
- 3The Francis Crick Institute, London, United Kingdom
| | | | - Gavin Kelly
- 3The Francis Crick Institute, London, United Kingdom
| | - Charles Swanton
- 2University College London Cancer Institute, University College London, London, United Kingdom
| | - Kazufumi Honda
- 1Institute for Advanced Medical Sciences, Nippon Medical University, Tokyo, Japan
| | - Erik Sahai
- 3The Francis Crick Institute, London, United Kingdom
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17
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Martin SB, Polubothu S, Bruzos A, Bulstrode N, Kelly G, Kinsler V. Abstract 2014: Mosaic BRAF fusions are a recurrent cause of multiple congenital melanocytic naevi. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Congenital melanocytic naevi (CMN) are moles present at birth, and when multiple or very extensive can involve other organ systems as well as predisposing to melanoma. Some CMN patients develop a highly proliferative multinodular phenotype leading to chronic intense pruritus, and the causes for that specific phenotype progression are poorly understood. Genotypically CMN are mosaic single gene disorders. Thus far only two recurrent variants have been described as clearly causative: NRAS missense variants affecting codon 61 accounting for 68% of cases, and BRAF missense variants affecting codon 600 accounting for 7% of cases. Small numbers of cases of CMN have been reported to carry gene-fusions, and in 2 cases in the world literature (one BRAF-fusion and one RAF1-fusion) these have been shown to be clonal and therefore likely causal. We sought to address the issue of causation of the remaining 25%. From an initial large cohort study, skin biopsies from 19 patients were shown to be double wildtype for NRAS/BRAF and had sufficient tissue for further study after deep whole exome sequencing. These 19 samples then underwent transcriptome-wide paired-end RNA sequencing with bioinformatics analysis (STAR-Fusion v1.6 and Fusion Inspector v2.3) for gene fusion transcripts. 11/19 patients were found to have BRAFgene fusions, of which 7 had the multinodular proliferative phenotype. Fusions were confirmed on Sanger sequencing of the cDNA across the fusion junction, specifically demonstrated in 8 children from more than one separate skin lesion, confirming clonality. In the fusions identified, BRAF was fused to 11 different partner genes (GOLGA4, QKI, STRN3, AGAP3, MKRN2, PHIP, LCA5, EEA1, AKAP9, SEC31A, MIER3). This resulted in loss of the 5’ regulatory domain of BRAF but preservation of the kinase domain, such that expression was driven by the 5’ fusion partner. This structure follows the pattern of somatic BRAF-fusions reported previously in solid tumors including melanoma. Potential dimerization domains in the partner genes were identified in 9 cases. We identify here mosaic BRAF fusions as a recurrent cause of multiple CMN allowing genetic diagnosis in a further 15% of cases and linking this genotype to a highly proliferative pruritic phenotype. In vitro data from melanoma cell lines have suggested that higher expression levels of the fusion protein as well as dimerization domains in the partner gene correlate with resistance and/or paradoxical MAP-kinase activation after treatment with RAF and MEK inhibitors. This may have implications for the use of targeted therapies for attempted reduction of the nodular phenotype, or where melanoma arises in CMN patients caused by mosaic BRAF-fusions.
Citation Format: Sara Barberan Martin, Satyamaanasa Polubothu, Alicia Bruzos, Neil Bulstrode, Gavin Kelly, Veronica Kinsler. Mosaic BRAF fusions are a recurrent cause of multiple congenital melanocytic naevi [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2014.
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Affiliation(s)
| | | | | | - Neil Bulstrode
- 2Great Ormond St Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Gavin Kelly
- 1Francis Crick Institute, London, United Kingdom
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18
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Zhang L, Pickard K, Jenei V, Bullock MD, Bruce A, Mitter R, Kelly G, Paraskeva C, Strefford J, Primrose J, Thomas GJ, Packham G, Mirnezami AH. Editor's Note: miR-153 Supports Colorectal Cancer Progression via Pleiotropic Effects That Enhance Invasion and Chemotherapeutic Resistance. Cancer Res 2022; 82:1669. [DOI: 10.1158/0008-5472.can-22-0501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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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20
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Mauger M, Kelly G, Annandale CH, Robertson ID, Waichigo FK, Aleri JW. Anthelmintic resistance of gastrointestinal nematodes in dairy calves within a pasture-based production system of south West Western Australia. Aust Vet J 2022; 100:283-291. [PMID: 35383394 PMCID: PMC9542819 DOI: 10.1111/avj.13162] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 02/15/2022] [Accepted: 03/20/2022] [Indexed: 11/30/2022]
Abstract
The objective of this study was to determine the prevalence of gastrointestinal nematodes among post‐weaned calves aged between 4 and 12 months old within a pasture‐based system of south west Australia and quantify the level of anthelmintic resistance. Pre‐treatment FECs were monitored on 14 dairy farms. Anthelmintic resistance was assessed on 11 of the farms. Control FECs were compared with anthelmintic FECs at 14 days post‐treatment with doramectin (injectable), levamisole (oral), fenbendazole (oral) and a levamisole/abamectin combination (pour‐on). Results demonstrate a strong level of anthelmintic resistance, with at least one class of anthelmintic failing to achieve a 95% reduction in FEC in one or more gastrointestinal nematode species. Doramectin was fully effective against Ostertagia, but C. oncophora displayed resistance in 91% of the farms. Conversely, levamisole was fully effective against C. oncophora, but Ostertagia displayed resistance in 80% of the farms. Fenbendazole resistance was present in both C. onocphora and Ostertagia in 64% and 70% of the farms, respectively. Trichostrongylus showed low resistance, occurring in doramectin (14%) and levamisole/abamectin combination (14%). This study confirms that anthelmintic resistance is common. Regular FEC reduction testing is recommended to monitor and guide decision‐making for appropriate anthelmintic usage.
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Affiliation(s)
- M Mauger
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - G Kelly
- Boehringer Ingelheim Animal Health Australia Pty. Ltd., North Ryde, New South Wales, Australia
| | - C H Annandale
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - I D Robertson
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - F K Waichigo
- Brunswick Veterinary Services, Brunswick Junction, Western Australia, Australia
| | - J W Aleri
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia.,Centre for Animal Production and Health, Future Foods Institute, Murdoch University, Murdoch, Western Australia, Australia
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21
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Shah K, Maradana MR, Joaquina Delàs M, Metidji A, Graelmann F, Llorian M, Chakravarty P, Li Y, Tolaini M, Shapiro M, Kelly G, Cheshire C, Bhurta D, Bharate SB, Stockinger B. Cell-intrinsic Aryl Hydrocarbon Receptor signalling is required for the resolution of injury-induced colonic stem cells. Nat Commun 2022; 13:1827. [PMID: 35383166 PMCID: PMC8983642 DOI: 10.1038/s41467-022-29098-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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: 08/19/2021] [Accepted: 02/23/2022] [Indexed: 12/17/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is an environmental sensor that integrates microbial and dietary cues to influence physiological processes within the intestinal microenvironment, protecting against colitis and colitis-associated colorectal cancer development. Rapid tissue regeneration upon injury is important for the reinstatement of barrier integrity and its dysregulation promotes malignant transformation. Here we show that AHR is important for the termination of the regenerative response and the reacquisition of mature epithelial cell identity post injury in vivo and in organoid cultures in vitro. Using an integrative multi-omics approach in colon organoids, we show that AHR is required for timely termination of the regenerative response through direct regulation of transcription factors involved in epithelial cell differentiation as well as restriction of chromatin accessibility to regeneration-associated Yap/Tead transcriptional targets. Safeguarding a regulated regenerative response places AHR at a pivotal position in the delicate balance between controlled regeneration and malignant transformation. Rapid intestinal regeneration after injury is critical to maintain barrier integrity and homeostasis, but must be tightly controlled to prevent tumorigenesis. Here they show that the aryl hydrocarbon receptor is required to terminate the regenerative response after wound healing.
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Affiliation(s)
| | | | | | - Amina Metidji
- Department of Oncology, St Jude Children's Hospital, Memphis, TN, USA
| | - Frederike Graelmann
- Immunology and Environment, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | | | | | - Ying Li
- The Francis Crick Institute, London, UK
| | | | | | | | | | - Deendyal Bhurta
- Natural Products & Medicinal Chemistry Division, CSIR - Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Sandip B Bharate
- Natural Products & Medicinal Chemistry Division, CSIR - Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
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22
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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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23
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Carr EJ, Wu M, Harvey R, Billany RE, Wall EC, Kelly G, Howell M, Kassiotis G, Swanton C, Gandhi S, Bauer DL, Graham-Brown MP, Jones RB, Smith RM, McAdoo S, Willicombe M, Beale R. Omicron neutralising antibodies after COVID-19 vaccination in haemodialysis patients. Lancet 2022; 399:800-802. [PMID: 35065703 PMCID: PMC8776276 DOI: 10.1016/s0140-6736(22)00104-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 02/07/2023]
Affiliation(s)
| | - Mary Wu
- The Francis Crick Institute, London NW1 1AT, UK
| | - Ruth Harvey
- The Francis Crick Institute, London NW1 1AT, UK
| | - Roseanne E Billany
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Department of Renal Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK; NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Emma C Wall
- The Francis Crick Institute, London NW1 1AT, UK
| | - Gavin Kelly
- The Francis Crick Institute, London NW1 1AT, UK
| | | | | | | | | | | | - Matthew Pm Graham-Brown
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Department of Renal Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK; NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Rachel B Jones
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK; Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rona M Smith
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK; Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Stephen McAdoo
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK; Renal and Transplant Centre, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | - Michelle Willicombe
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK; Renal and Transplant Centre, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | - Rupert Beale
- The Francis Crick Institute, London NW1 1AT, UK; UCL Dept of Renal Medicine, Royal Free Hospital, London, UK.
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24
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Wu M, Wall EC, Carr EJ, Harvey R, Townsley H, Mears HV, Adams L, Kjaer S, Kelly G, Warchal S, Sawyer C, Kavanagh C, Queval CJ, Ngai Y, Hatipoglu E, Ambrose K, Hindmarsh S, Beale R, Gamblin S, Howell M, Kassiotis G, Libri V, Williams B, Gandhi S, Swanton C, Bauer DL. Three-dose vaccination elicits neutralising antibodies against omicron. Lancet 2022; 399:715-717. [PMID: 35065005 PMCID: PMC8769665 DOI: 10.1016/s0140-6736(22)00092-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 12/21/2022]
Affiliation(s)
- Mary Wu
- The Francis Crick Institute, London NW1 1AT, 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
| | | | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London, UK
| | - Hermaleigh Townsley
- 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
| | | | - Lorin Adams
- Worldwide Influenza Centre, The Francis Crick Institute, London, UK
| | - Svend Kjaer
- 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; 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
| | - 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
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25
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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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26
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Fendler A, Shepherd ST, Au L, Wilkinson KA, Wu M, Byrne F, Cerrone M, Schmitt AM, Joharatnam-Hogan N, Shum B, Tippu Z, Rzeniewicz K, Boos LA, Harvey R, Carlyle E, Edmonds K, Del Rosario L, Sarker S, Lingard K, Mangwende M, Holt L, Ahmod H, Korteweg J, Foley T, Bazin J, Gordon W, Barber T, Emslie-Henry A, Xie W, Gerard CL, Deng D, Wall EC, Agua-Doce A, Namjou S, Caidan S, Gavrielides M, MacRae JI, Kelly G, Peat K, Kelly D, Murra A, Kelly K, O’Flaherty M, Dowdie L, Ash N, Gronthoud F, Shea RL, Gardner G, Murray D, Kinnaird F, Cui W, Pascual J, Rodney S, Mencel J, Curtis O, Stephenson C, Robinson A, Oza B, Farag S, Leslie I, Rogiers A, Iyengar S, Ethell M, Messiou C, Cunningham D, Chau I, Starling N, Turner N, Welsh L, van As N, Jones RL, Droney J, Banerjee S, Tatham KC, O’Brien M, Harrington K, Bhide S, Okines A, Reid A, Young K, Furness AJ, Pickering L, Swanton C, Gandhi S, Gamblin S, Bauer DLV, Kassiotis G, Kumar S, Yousaf N, Jhanji S, Nicholson E, Howell M, Walker S, Wilkinson RJ, Larkin J, Turajlic S. Adaptive immunity and neutralizing antibodies against SARS-CoV-2 variants of concern following vaccination in patients with cancer: The CAPTURE study. Nat Cancer 2021; 2:1321-1337. [PMID: 34950880 PMCID: PMC7612125 DOI: 10.1038/s43018-021-00274-w] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [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] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/17/2021] [Indexed: 12/13/2022]
Abstract
CAPTURE (NCT03226886) is a prospective cohort study of COVID-19 immunity in patients with cancer. Here we evaluated 585 patients following administration of two doses of BNT162b2 or AZD1222 vaccines, administered 12 weeks apart. Seroconversion rates after two doses were 85% and 59% in patients with solid and hematological malignancies, respectively. A lower proportion of patients had detectable neutralizing antibody titers (NAbT) against SARS-CoV-2 variants of concern (VOCs) vs wildtype (WT). Patients with hematological malignancies were more likely to have undetectable NAbT and had lower median NAbT vs solid cancers against both WT and VOCs. In comparison with individuals without cancer, patients with haematological, but not solid, malignancies had reduced NAb responses. Seroconversion showed poor concordance with NAbT against VOCs. Prior SARS-CoV-2 infection boosted NAb response including against VOCs, and anti-CD20 treatment was associated with undetectable NAbT. Vaccine-induced T-cell responses were detected in 80% of patients, and were comparable between vaccines or cancer types. Our results have implications for the management of cancer patients during the ongoing COVID-19 pandemic.
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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
| | - 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, Cape Town, Republic of South Africa
| | - Mary Wu
- Wellcome Center for Infectious Disease Research in Africa, University of Cape Town, Observatory, Cape Town, Republic of South Africa
| | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Maddalena Cerrone
- Tuberculosis Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Andreas M. Schmitt
- 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
| | - Zayd Tippu
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Karolina Rzeniewicz
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Laura Amanda Boos
- 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
| | - Sarah Sarker
- 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
| | - Jessica Bazin
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - William Gordon
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, 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
| | - Wenyi Xie
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, NW1 1AT, 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
| | - Emma C. Wall
- University College London Hospitals NHS Foundation Trust Biomedical Research Centre, London, NW1 1AT, UK
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Experimental Histopathology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ana Agua-Doce
- Flow Cytometry Scientific Technology Platform, 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
| | - Lauren Dowdie
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Natalie Ash
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Firza Gronthoud
- Department of Pathology, The Royal Marsden NHS Foundation Trust, London, NW1 1AT, 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
| | - Fiona Kinnaird
- Clinical Trials Unit, The Royal Marsden NHS Foundation Trust, London, SM2 5PT, UK
| | - Wanyuan Cui
- Lung Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Javier Pascual
- Breast Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Simon Rodney
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Justin Mencel
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey SM2 5PT
| | - Olivia Curtis
- Lung Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Clemency Stephenson
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Anna Robinson
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Bhavna Oza
- 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
| | - Isla Leslie
- 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
| | - Sunil Iyengar
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Mark Ethell
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Christina Messiou
- Department of Radiology, 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
| | - Ian Chau
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey SM2 5PT
| | - Naureen Starling
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey SM2 5PT
| | - Nicholas Turner
- Breast Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Liam Welsh
- Neuro-oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Nicholas van As
- Clinical Oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Robin L. Jones
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, SW3 6JJ, UK
| | - Joanne Droney
- Palliative Medicine, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Susana Banerjee
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Kate C. Tatham
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Mary O’Brien
- Lung Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Kevin Harrington
- Head and Neck, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
- Targeted Therapy Team, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Shreerang Bhide
- Head and Neck, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
- Targeted Therapy Team, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Alicia Okines
- Breast Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
- Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Alison Reid
- Uro-oncology unit, The Royal Marsden NHS Foundation Trust, Surrey, SM2 5PT
| | - 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
| | - 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
| | - Steve Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Experimental Histopathology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - David LV 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
| | - Sacheen Kumar
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey SM2 5PT
| | - 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
| | - Emma Nicholson
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, 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
| | - 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, Cape Town, Republic of South Africa
- Department of Infectious Disease, Imperial College London, London, 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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27
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van Maldegem F, Valand K, Cole M, Patel H, Angelova M, Rana S, Colliver E, Enfield K, Bah N, Kelly G, Tsang VSK, Mugarza E, Moore C, Hobson P, Levi D, Molina-Arcas M, Swanton C, Downward J. Characterisation of tumour microenvironment remodelling following oncogene inhibition in preclinical studies with imaging mass cytometry. Nat Commun 2021; 12:5906. [PMID: 34625563 PMCID: PMC8501076 DOI: 10.1038/s41467-021-26214-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 03/05/2021] [Accepted: 09/20/2021] [Indexed: 01/23/2023] Open
Abstract
Mouse models are critical in pre-clinical studies of cancer therapy, allowing dissection of mechanisms through chemical and genetic manipulations that are not feasible in the clinical setting. In studies of the tumour microenvironment (TME), multiplexed imaging methods can provide a rich source of information. However, the application of such technologies in mouse tissues is still in its infancy. Here we present a workflow for studying the TME using imaging mass cytometry with a panel of 27 antibodies on frozen mouse tissues. We optimise and validate image segmentation strategies and automate the process in a Nextflow-based pipeline (imcyto) that is scalable and portable, allowing for parallelised segmentation of large multi-image datasets. With these methods we interrogate the remodelling of the TME induced by a KRAS G12C inhibitor in an immune competent mouse orthotopic lung cancer model, highlighting the infiltration and activation of antigen presenting cells and effector cells.
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Affiliation(s)
- Febe van Maldegem
- Oncogene Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ, Amsterdam, The Netherlands.
| | - Karishma Valand
- Oncogene Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Megan Cole
- Oncogene Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sareena Rana
- Oncogene Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Lung Cancer Group, Division of Molecular Pathology, Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Katey Enfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Nourdine Bah
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Victoria Siu Kwan Tsang
- Oncogene Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Edurne Mugarza
- Oncogene Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Christopher Moore
- Oncogene Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Philip Hobson
- Flow Cytometry Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Dina Levi
- Flow Cytometry Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Miriam Molina-Arcas
- Oncogene Biology Laboratory, 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, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Lung Cancer Group, Division of Molecular Pathology, Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
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28
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Carr EJ, Wu M, Harvey R, Wall EC, Kelly G, Hussain S, Howell M, Kassiotis G, Swanton C, Gandhi S, Bauer DL, Billany RE, Graham-Brown MP, Beckett J, Bull K, Shankar S, Henderson S, Motallebzadeh R, Salama AD, Harper L, Mark PB, McAdoo S, Willicombe M, Beale R. Neutralising antibodies after COVID-19 vaccination in UK haemodialysis patients. Lancet 2021; 398:1038-1041. [PMID: 34391504 PMCID: PMC8360704 DOI: 10.1016/s0140-6736(21)01854-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
| | - Mary Wu
- The Francis Crick Institute, London NW1 1AT, UK
| | - Ruth Harvey
- The Francis Crick Institute, London NW1 1AT, UK
| | - Emma C Wall
- The Francis Crick Institute, London NW1 1AT, UK
| | - Gavin Kelly
- The Francis Crick Institute, London NW1 1AT, UK
| | | | | | | | | | | | | | - Roseanne E Billany
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Department of Renal Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK; NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Matthew Pm Graham-Brown
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Department of Renal Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK; NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Joseph Beckett
- Transplantation Research & Immunology Group, University of Oxford, Oxford, UK
| | - Katherine Bull
- Nuffield Department of Surgical Sciences and Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sushma Shankar
- Transplantation Research & Immunology Group, University of Oxford, Oxford, UK; Oxford Transplant Centre, University of Oxford, Oxford, UK
| | - Scott Henderson
- UCL Department of Renal Medicine, Royal Free Hospital, London, UK
| | - Reza Motallebzadeh
- UCL Department of Renal Medicine, Royal Free Hospital, London, UK; Research Department of Surgical Biotechnology, Division of Surgery and Interventional Science, University College London, London, UK
| | - Alan D Salama
- UCL Department of Renal Medicine, Royal Free Hospital, London, UK
| | - Lorraine Harper
- Institute of Applied Health Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; Department of Nephrology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Patrick B Mark
- Glasgow Renal and Transplant Unit, Queen Elizabeth University Hospital, Glasgow, UK; Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Stephen McAdoo
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London UK; Renal and Transplant Centre, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | - Michelle Willicombe
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London UK; Renal and Transplant Centre, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | - Rupert Beale
- The Francis Crick Institute, London NW1 1AT, UK; UCL Department of Renal Medicine, Royal Free Hospital, London, UK.
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29
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Loss L, Kelly G, Koizumi N, Siddique AB, Shreve J, Markowiak SF, Nazzal M, Ortiz J. Rankings From US News and World Report Have Minimal Correlation With Kidney and Liver Transplant Recipient Survival Results From Retrospective Data. EXP CLIN TRANSPLANT 2021; 19:1014-1022. [PMID: 34309500 DOI: 10.6002/ect.2021.0043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVES Increased demand for quality health care has led to lay-press ranking systems, such as the ranking from US News and World Report (US News). Their "Best Hospitals" publication advertises itself as the go-to resource for patients seeking care in a number of specialty areas. We sought to test the relationship between US News rankings and transplant outcomes. MATERIALS AND METHODS Using data from 2014 to 2018, we compared outcomes from the Scientific Registry of Transplant Recipients database for liver and kidney transplants against US News-ranked centers using the categories "Nephrology" and "GI Surgery and Gastroenterology" as substitutes, as US News does not rank transplant centers specifically. P < .05 was set as significant. RESULTS Using hazard ratio data, we found that kidney transplant center rank had only a small impact on postoperative outcomes in terms of patient survival (hazard ratio = 0.996, P = .049) but had no impact on graft survival (hazard ratio = 0.997, P = .077). In addition, liver transplant center rank had no impact on liver graft survival (hazard ratio = 1.003, P = .304). The impact of hospital ranking on survival was minimal compared with other variables. CONCLUSIONS The US News rankings for "Nephrology" and "GI Surgery and Gastroenterology" have minimal values as a measure of liver and kidney transplant outcomes, highlighting that these lay press rankings are not useful to the unique transplant patient population and that providers should help guide patients to transplant-specific resources.
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Affiliation(s)
- Lindsey Loss
- From the University of Toledo Medical Center, Toledo, Ohio, USA.,From the Oregon Health and Science University, Portland, Oregon,USA
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30
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Wall EC, Wu M, Harvey R, Kelly G, Warchal S, Sawyer C, Daniels R, Adams L, Hobson P, Hatipoglu E, Ngai Y, Hussain S, Ambrose K, Hindmarsh S, Beale R, Riddell A, Gamblin S, Howell M, Kassiotis G, Libri V, Williams B, Swanton C, Gandhi S, Bauer DL. AZD1222-induced neutralising antibody activity against SARS-CoV-2 Delta VOC. Lancet 2021; 398:207-209. [PMID: 34197809 PMCID: PMC8238446 DOI: 10.1016/s0140-6736(21)01462-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022]
Affiliation(s)
- Emma C Wall
- Francis Crick Institute, London NW1 1AT, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre, London, UK; NIHR UCLH Clinical Research Facility, London, UK
| | - Mary Wu
- Francis Crick Institute, London NW1 1AT, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | - Rupert Beale
- Francis Crick Institute, London NW1 1AT, UK; NIHR UCLH Clinical Research Facility, London, UK; University College London, London, UK
| | | | | | | | - George Kassiotis
- 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, London, UK; 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, London, UK; NIHR UCLH Clinical Research Facility, London, UK; University College London, London, UK
| | - Charles Swanton
- Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Sonia Gandhi
- Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
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31
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Ruiz EJ, Lan L, Diefenbacher ME, Riising EM, Da Costa C, Chakraborty A, Hoeck JD, Spencer-Dene B, Kelly G, David JP, Nye E, Downward J, Behrens A. JunD, not c-Jun, is the AP-1 transcription factor required for Ras-induced lung cancer. JCI Insight 2021; 6:e124985. [PMID: 34236045 PMCID: PMC8410048 DOI: 10.1172/jci.insight.124985] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 09/18/2018] [Accepted: 05/28/2021] [Indexed: 12/15/2022] Open
Abstract
The AP-1 transcription factor c-Jun is required for Ras-driven tumorigenesis in many tissues and is considered as a classical proto-oncogene. To determine the requirement for c-Jun in a mouse model of K-RasG12D-induced lung adenocarcinoma, we inducibly deleted c-Jun in the adult lung. Surprisingly, we found that inactivation of c-Jun, or mutation of its JNK phosphorylation sites, actually increased lung tumor burden. Mechanistically, we found that protein levels of the Jun family member JunD were increased in the absence of c-Jun. In c-Jun-deficient cells, JunD phosphorylation was increased, and expression of a dominant-active JNKK2-JNK1 transgene further increased lung tumor formation. Strikingly, deletion of JunD completely abolished Ras-driven lung tumorigenesis. This work identifies JunD, not c-Jun, as the crucial substrate of JNK signaling and oncogene required for Ras-induced lung cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Gavin Kelly
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, United Kingdom
| | - Jean-Pierre David
- Institute of Osteology and Biomechanics, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Emma Nye
- Experimental Histopathology, and
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Axel Behrens
- Adult Stem Cell Laboratory.,Cancer Stem Cell Laboratory, Institute of Cancer Research, London, United Kingdom.,Imperial College, Division of Cancer, Department of Surgery and Cancer, London, United Kingdom.,Convergence Science Centre, Imperial College, London, United Kingdom
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32
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Lancaster L, Patel H, Kelly G, Uhlmann F. A role for condensin in mediating transcriptional adaptation to environmental stimuli. Life Sci Alliance 2021; 4:e202000961. [PMID: 34083394 PMCID: PMC8200293 DOI: 10.26508/lsa.202000961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 11/17/2020] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 01/04/2023] Open
Abstract
Nuclear organisation shapes gene regulation; however, the principles by which three-dimensional genome architecture influences gene transcription are incompletely understood. Condensin is a key architectural chromatin constituent, best known for its role in mitotic chromosome condensation. Yet at least a subset of condensin is bound to DNA throughout the cell cycle. Studies in various organisms have reported roles for condensin in transcriptional regulation, but no unifying mechanism has emerged. Here, we use rapid conditional condensin depletion in the budding yeast Saccharomyces cerevisiae to study its role in transcriptional regulation. We observe a large number of small gene expression changes, enriched at genes located close to condensin-binding sites, consistent with a possible local effect of condensin on gene expression. Furthermore, nascent RNA sequencing reveals that transcriptional down-regulation in response to environmental stimuli, in particular to heat shock, is subdued without condensin. Our results underscore the multitude by which an architectural chromosome constituent can affect gene regulation and suggest that condensin facilitates transcriptional reprogramming as part of adaptation to environmental changes.
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Affiliation(s)
- Lucy Lancaster
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
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33
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Wall EC, Wu M, Harvey R, Kelly G, Warchal S, Sawyer C, Daniels R, Hobson P, Hatipoglu E, Ngai Y, Hussain S, Nicod J, Goldstone R, Ambrose K, Hindmarsh S, Beale R, Riddell A, Gamblin S, Howell M, Kassiotis G, Libri V, Williams B, Swanton C, Gandhi S, Bauer DL. Neutralising antibody activity against SARS-CoV-2 VOCs B.1.617.2 and B.1.351 by BNT162b2 vaccination. Lancet 2021; 397:2331-2333. [PMID: 34090624 PMCID: PMC8175044 DOI: 10.1016/s0140-6736(21)01290-3] [Citation(s) in RCA: 375] [Impact Index Per Article: 125.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 06/02/2021] [Indexed: 01/01/2023]
Affiliation(s)
- Emma C Wall
- Francis Crick Institute, London, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre, London, UK; NIHR UCLH Clinical Research Facility, London, UK
| | - Mary Wu
- Francis Crick Institute, London, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Rupert Beale
- Francis Crick Institute, London, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre, London, UK; NIHR UCLH Clinical Research Facility, London, UK
| | | | | | | | - George Kassiotis
- Francis Crick Institute, London, 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, London, UK; 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, London, UK; NIHR UCLH Clinical Research Facility, London, UK; University College London, London, UK
| | | | - Sonia Gandhi
- Francis Crick Institute, London, UK; University College London, London, UK
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34
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Bosworth K, Mustafa Y, Aukland M, Bhat A, Kelly G. P.77 Skin-to-skin care during caesarean section in two obstetric units. Int J Obstet Anesth 2021. [DOI: 10.1016/j.ijoa.2021.103075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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35
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Ziff OJ, Taha DM, Crerar H, Clarke BE, Chakrabarti AM, Kelly G, Neeves J, Tyzack GE, Luscombe NM, Patani R. Reactive astrocytes in ALS display diminished intron retention. Nucleic Acids Res 2021; 49:3168-3184. [PMID: 33684213 PMCID: PMC8034657 DOI: 10.1093/nar/gkab115] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/13/2022] Open
Abstract
Reactive astrocytes are implicated in amyotrophic lateral sclerosis (ALS), although the mechanisms controlling reactive transformation are unknown. We show that decreased intron retention (IR) is common to human-induced pluripotent stem cell (hiPSC)-derived astrocytes carrying ALS-causing mutations in VCP, SOD1 and C9orf72. Notably, transcripts with decreased IR and increased expression are overrepresented in reactivity processes including cell adhesion, stress response and immune activation. This was recapitulated in public-datasets for (i) hiPSC-derived astrocytes stimulated with cytokines to undergo reactive transformation and (ii) in vivo astrocytes following selective deletion of TDP-43. We also re-examined public translatome sequencing (TRAP-seq) of astrocytes from a SOD1 mouse model, which revealed that transcripts upregulated in translation significantly overlap with transcripts exhibiting decreased IR. Using nucleocytoplasmic fractionation of VCP mutant astrocytes coupled with mRNA sequencing and proteomics, we identify that decreased IR in nuclear transcripts is associated with enhanced nonsense mediated decay and increased cytoplasmic expression of transcripts and proteins regulating reactive transformation. These findings are consistent with a molecular model for reactive transformation in astrocytes whereby poised nuclear reactivity-related IR transcripts are spliced, undergo nuclear-to-cytoplasmic translocation and translation. Our study therefore provides new insights into the molecular regulation of reactive transformation in astrocytes.
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Affiliation(s)
- Oliver J Ziff
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK
| | - Doaa M Taha
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,Department of Zoology, Faculty of Science, Alexandria University, Alexandria 21511, Egypt
| | - Hamish Crerar
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Benjamin E Clarke
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Anob M Chakrabarti
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jacob Neeves
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Giulia E Tyzack
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK.,Okinawa Institute of Science & Technology Graduate University, Okinawa 904-0495, Japan
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK
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Hellewell J, Russell TW, Beale R, Kelly G, Houlihan C, Nastouli E, Kucharski AJ. Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections. BMC Med 2021; 19:106. [PMID: 33902581 PMCID: PMC8075718 DOI: 10.1186/s12916-021-01982-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/07/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Routine asymptomatic testing using RT-PCR of people who interact with vulnerable populations, such as medical staff in hospitals or care workers in care homes, has been employed to help prevent outbreaks among vulnerable populations. Although the peak sensitivity of RT-PCR can be high, the probability of detecting an infection will vary throughout the course of an infection. The effectiveness of routine asymptomatic testing will therefore depend on testing frequency and how PCR detection varies over time. METHODS We fitted a Bayesian statistical model to a dataset of twice weekly PCR tests of UK healthcare workers performed by self-administered nasopharyngeal swab, regardless of symptoms. We jointly estimated times of infection and the probability of a positive PCR test over time following infection; we then compared asymptomatic testing strategies by calculating the probability that a symptomatic infection is detected before symptom onset and the probability that an asymptomatic infection is detected within 7 days of infection. RESULTS We estimated that the probability that the PCR test detected infection peaked at 77% (54-88%) 4 days after infection, decreasing to 50% (38-65%) by 10 days after infection. Our results suggest a substantially higher probability of detecting infections 1-3 days after infection than previously published estimates. We estimated that testing every other day would detect 57% (33-76%) of symptomatic cases prior to onset and 94% (75-99%) of asymptomatic cases within 7 days if test results were returned within a day. CONCLUSIONS Our results suggest that routine asymptomatic testing can enable detection of a high proportion of infected individuals early in their infection, provided that the testing is frequent and the time from testing to notification of results is sufficiently fast.
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Affiliation(s)
- Joel Hellewell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Timothy W Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute; Division of Medicine, UCL, London, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Catherine Houlihan
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Infection and Immunity, University College London, London, UK
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Eleni Nastouli
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Adam J Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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Collart C, Ciccarelli A, Ivanovitch K, Rosewell I, Kumar S, Kelly G, Edwards A, Smith JC. The migratory pathways of the cells that form the endocardium, dorsal aortae, and head vasculature in the mouse embryo. BMC Dev Biol 2021; 21:8. [PMID: 33752600 PMCID: PMC7986287 DOI: 10.1186/s12861-021-00239-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/12/2021] [Indexed: 11/25/2022]
Abstract
Background Vasculogenesis in amniotes is often viewed as two spatially and temporally distinct processes, occurring in the yolk sac and in the embryo. However, the spatial origins of the cells that form the primary intra-embryonic vasculature remain uncertain. In particular, do they obtain their haemato-endothelial cell fate in situ, or do they migrate from elsewhere? Recently developed imaging techniques, together with new Tal1 and existing Flk1 reporter mouse lines, have allowed us to investigate this question directly, by visualising cell trajectories live and in three dimensions. Results We describe the pathways that cells follow to form the primary embryonic circulatory system in the mouse embryo. In particular, we show that Tal1-positive cells migrate from within the yolk sac, at its distal border, to contribute to the endocardium, dorsal aortae and head vasculature. Other Tal1 positive cells, similarly activated within the yolk sac, contribute to the yolk sac vasculature. Using single-cell transcriptomics and our imaging, we identify VEGF and Apela as potential chemo-attractants that may regulate the migration into the embryo. The dorsal aortae and head vasculature are known sites of secondary haematopoiesis; given the common origins that we observe, we investigate whether this is also the case for the endocardium. We discover cells budding from the wall of the endocardium with high Tal1 expression and diminished Flk1 expression, indicative of an endothelial to haematopoietic transition. Conclusions In contrast to the view that the yolk sac and embryonic circulatory systems form by two separate processes, our results indicate that Tal1-positive cells from the yolk sac contribute to both vascular systems. It may be that initial Tal1 activation in these cells is through a common mechanism. Supplementary Information The online version contains supplementary material available at 10.1186/s12861-021-00239-3.
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Affiliation(s)
- C Collart
- Developmental Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - A Ciccarelli
- Advanced Light Microscopy Facility, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - K Ivanovitch
- Developmental Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - I Rosewell
- Genetic Modification Service, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - S Kumar
- Advanced Light Microscopy Facility, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Photonics Group, 606 Blackett Laboratory, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - G Kelly
- Bioinformatics and Biostatistics Facility, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - A Edwards
- Advanced Sequencing Facility, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - J C Smith
- Developmental Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
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38
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Wilkinson KA, Schneider-Luftman D, Lai R, Barrington C, Jhilmeet N, Lowe DM, Kelly G, Wilkinson RJ. Antiretroviral Treatment-Induced Decrease in Immune Activation Contributes to Reduced Susceptibility to Tuberculosis in HIV-1/Mtb Co-infected Persons. Front Immunol 2021; 12:645446. [PMID: 33746987 PMCID: PMC7973093 DOI: 10.3389/fimmu.2021.645446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 12/23/2020] [Accepted: 02/10/2021] [Indexed: 12/27/2022] Open
Abstract
Antiretroviral treatment (ART) reduces the risk of developing active tuberculosis (TB) in HIV-1 co-infected persons. In order to understand host immune responses during ART in the context of Mycobacterium tuberculosis (Mtb) sensitization, we performed RNAseq analysis of whole blood-derived RNA from individuals with latent TB infection coinfected with HIV-1, during the first 6 months of ART. A significant fall in RNA sequence abundance of the Hallmark IFN-alpha, IFN-gamma, IL-6/JAK/STAT3 signaling, and inflammatory response pathway genes indicated reduced immune activation and inflammation at 6 months of ART compared to day 0. Further exploratory evaluation of 65 soluble analytes in plasma confirmed the significant decrease of inflammatory markers after 6 months of ART. Next, we evaluated 30 soluble analytes in QuantiFERON Gold in-tube (QFT) samples from the Ag stimulated and Nil tubes, during the first 6 months of ART in 30 patients. There was a significant decrease in IL-1alpha and IL-1beta (Ag-Nil) concentrations as well as MCP-1 (Nil), supporting decreased immune activation and inflammation. At the same time, IP-10 (Ag-nil) concentrations significantly increased, together with chemokine receptor-expressing CD4 T cell numbers. Our data indicate that ART-induced decrease in immune activation combined with improved antigen responsiveness may contribute to reduced susceptibility to tuberculosis in HIV-1/Mtb co-infected persons.
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Affiliation(s)
- Katalin A Wilkinson
- Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom.,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Rachel Lai
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | | | - Nishtha Jhilmeet
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - David M Lowe
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Gavin Kelly
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, United Kingdom
| | - Robert J Wilkinson
- Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom.,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Department of Infectious Disease, Imperial College London, London, United Kingdom
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39
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Magri C, Schramme M, Nottrott K, Schweizer‐Gorgas D, Segard E, Kelly G, Schumacher J. Coronoidectomy as a treatment for mandibular immobility caused by fracture of the coronoid process in three horses. EQUINE VET EDUC 2020. [DOI: 10.1111/eve.13396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C. Magri
- Clinéquine VetAgro Sup Marcy l’Etoile France
| | - M. Schramme
- Clinéquine VetAgro Sup Marcy l’Etoile France
| | - K. Nottrott
- Clinéquine VetAgro Sup Marcy l’Etoile France
| | - D. Schweizer‐Gorgas
- Section of Diagnostic Imaging Vetsuisse Faculty University of Berne Berne Switzerland
| | - E. Segard
- Clinéquine VetAgro Sup Marcy l’Etoile France
| | - G. Kelly
- Fethard Equine Hospital Fethard Tipperary Ireland
| | - J. Schumacher
- Department of Large Animal Clinical Sciences College of Veterinary Medicine University of Tennessee Knoxville Tennessee USA
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40
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East P, Kelly G, Biswas D, Hancock D, Swanton C, de Carne S, Downward J. Stratification method based on RAS pathway oncogenic activity predicts outcome in lung adenocarcinoma. Eur J Cancer 2020. [DOI: 10.1016/s0959-8049(20)31113-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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Touati SA, Hofbauer L, Jones AW, Snijders AP, Kelly G, Uhlmann F. Cdc14 and PP2A Phosphatases Cooperate to Shape Phosphoproteome Dynamics during Mitotic Exit. Cell Rep 2020; 29:2105-2119.e4. [PMID: 31722221 PMCID: PMC6857435 DOI: 10.1016/j.celrep.2019.10.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 03/11/2019] [Revised: 09/27/2019] [Accepted: 10/10/2019] [Indexed: 12/22/2022] Open
Abstract
Temporal control over protein phosphorylation and dephosphorylation is crucial for accurate chromosome segregation and for completion of the cell division cycle during exit from mitosis. In budding yeast, the Cdc14 phosphatase is thought to be a major regulator at this time, while in higher eukaryotes PP2A phosphatases take a dominant role. Here, we use time-resolved phosphoproteome analysis in budding yeast to evaluate the respective contributions of Cdc14, PP2ACdc55, and PP2ARts1. This reveals an overlapping requirement for all three phosphatases during mitotic progression. Our time-resolved phosphoproteome resource reveals how Cdc14 instructs the sequential pattern of phosphorylation changes, in part through preferential recognition of serine-based cyclin-dependent kinase (Cdk) substrates. PP2ACdc55 and PP2ARts1 in turn exhibit a broad substrate spectrum with some selectivity for phosphothreonines and a role for PP2ARts1 in sustaining Aurora kinase activity. These results illustrate synergy and coordination between phosphatases as they orchestrate phosphoproteome dynamics during mitotic progression. Cdc14, PP2ACdc55, and PP2ARts1 phosphatases cooperate during budding yeast mitosis Cdc14 targets serine Cdk motifs for rapid dephosphorylation PP2ACdc55 dephosphorylates Cdk and Plk substrates on threonine residues PP2ARts1 displays regulatory crosstalk with Aurora kinase
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Affiliation(s)
- Sandra A Touati
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Lorena Hofbauer
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrew W Jones
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Ambrosius P Snijders
- Mass Spectrometry Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Gavin Kelly
- Bioinformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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42
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Houlihan CF, Vora N, Byrne T, Lewer D, Kelly G, Heaney J, Gandhi S, Spyer MJ, Beale R, Cherepanov P, Moore D, Gilson R, Gamblin S, Kassiotis G, McCoy LE, Swanton C, Hayward A, Nastouli E. Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers. Lancet 2020; 396:e6-e7. [PMID: 32653078 PMCID: PMC7347344 DOI: 10.1016/s0140-6736(20)31484-7] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [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: 06/25/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Catherine F Houlihan
- Department of Clinical Virology, University College London Hospitals, London W1T 4EU, UK; Department of Infection and Immunity, University College London, London, UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Nina Vora
- Institute for Global Health, University College London, London, UK
| | - Thomas Byrne
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Dan Lewer
- Institute of Epidemiology and Healthcare, University College London, London, UK
| | | | - Judith Heaney
- Advanced Pathogen Diagnostics Unit, University College London Hospitals, London W1T 4EU, UK; Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sonia Gandhi
- Queen Square Institute of Neurology, University College London, London, UK; The Francis Crick Institute, London, UK
| | - Moira J Spyer
- Advanced Pathogen Diagnostics Unit, University College London Hospitals, London W1T 4EU, UK; Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Rupert Beale
- Division of Medicine, University College London Hospitals, London W1T 4EU, UK; The Francis Crick Institute, London, UK
| | - Peter Cherepanov
- The Francis Crick Institute, London, UK; Department of Medicine, Faculty of Medicine, Imperial College London, London, UK
| | - David Moore
- Cancer Institute, University College London, London, UK
| | - Richard Gilson
- Institute for Global Health, University College London, London, UK
| | | | - George Kassiotis
- The Francis Crick Institute, London, UK; Department of Medicine, Faculty of Medicine, Imperial College London, London, UK.
| | - Laura E McCoy
- Department of Infection and Immunity, University College London, London, UK
| | - Charles Swanton
- Macmillan Cancer Centre, University College London Hospitals, London W1T 4EU, UK; Cancer Institute, University College London, London, UK; The Francis Crick Institute, London, UK.
| | - Andrew Hayward
- Institute of Epidemiology and Healthcare, University College London, London, UK
| | - Eleni Nastouli
- Department of Clinical Virology, University College London Hospitals, London W1T 4EU, UK; Advanced Pathogen Diagnostics Unit, University College London Hospitals, London W1T 4EU, UK; Great Ormond Street Institute of Child Health, University College London, London, UK.
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43
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Kelly G, Hamilton C, Pool J. Investigating the use of rhythmic auditory stimulation for children with acquired brain injury. Physiotherapy 2020. [DOI: 10.1016/j.physio.2020.03.090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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44
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Garrod R, Kelly G, Randall S, Palanivel D. Best practice for serial casting to increase ankle range of movement following botulinum toxin in children with acquired brain Injury. Physiotherapy 2020. [DOI: 10.1016/j.physio.2020.03.306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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45
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Aegerter H, Kulikauskaite J, Crotta S, Patel H, Kelly G, Hessel EM, Mack M, Beinke S, Wack A. Influenza-induced monocyte-derived alveolar macrophages confer prolonged antibacterial protection. Nat Immunol 2020; 21:145-157. [PMID: 31932810 PMCID: PMC6983324 DOI: 10.1038/s41590-019-0568-x] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [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: 10/08/2018] [Accepted: 11/22/2019] [Indexed: 12/13/2022]
Abstract
Despite the prevalence and clinical importance of influenza, its long-term effect on lung immunity is unclear. Here we describe that following viral clearance and clinical recovery, at 1 month after infection with influenza, mice are better protected from Streptococcus pneumoniae infection due to a population of monocyte-derived alveolar macrophages (AMs) that produce increased interleukin-6. Influenza-induced monocyte-derived AMs have a surface phenotype similar to resident AMs but display a unique functional, transcriptional and epigenetic profile that is distinct from resident AMs. In contrast, influenza-experienced resident AMs remain largely similar to naive AMs. Thus, influenza changes the composition of the AM population to provide prolonged antibacterial protection. Monocyte-derived AMs persist over time but lose their protective profile. Our results help to understand how transient respiratory infections, a common occurrence in human life, can constantly alter lung immunity by contributing monocyte-derived, recruited cells to the AM population.
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Affiliation(s)
- Helena Aegerter
- Immunoregulation Laboratory, Francis Crick Institute, London, UK
| | | | - Stefania Crotta
- Immunoregulation Laboratory, Francis Crick Institute, London, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, Francis Crick Institute, London, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics, Francis Crick Institute, London, UK
| | - Edith M Hessel
- Refractory Respiratory Inflammation Discovery Performance Unit, Respiratory Therapy Area, GlaxoSmithKline, Stevenage, UK
| | - Matthias Mack
- Innere Medizin II-Nephrologie, Universitätsklinikum Regensburg, Regensburg, Germany
| | - Soren Beinke
- Refractory Respiratory Inflammation Discovery Performance Unit, Respiratory Therapy Area, GlaxoSmithKline, Stevenage, UK
| | - Andreas Wack
- Immunoregulation Laboratory, Francis Crick Institute, London, UK.
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46
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Jimeno R, Lebrusant-Fernandez M, Margreitter C, Lucas B, Veerapen N, Kelly G, Besra GS, Fraternali F, Spencer J, Anderson G, Barral P. Tissue-specific shaping of the TCR repertoire and antigen specificity of iNKT cells. eLife 2019; 8:51663. [PMID: 31841113 PMCID: PMC6930077 DOI: 10.7554/elife.51663] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 09/05/2019] [Accepted: 12/15/2019] [Indexed: 12/19/2022] Open
Abstract
Tissue homeostasis is critically dependent on the function of tissue-resident lymphocytes, including lipid-reactive invariant natural killer T (iNKT) cells. Yet, if and how the tissue environment shapes the antigen specificity of iNKT cells remains unknown. By analysing iNKT cells from lymphoid tissues of mice and humans we demonstrate that their T cell receptor (TCR) repertoire is highly diverse and is distinct for cells from various tissues resulting in differential lipid-antigen recognition. Within peripheral tissues iNKT cell recent thymic emigrants exhibit a different TCR repertoire than mature cells, suggesting that the iNKT population is shaped after arrival to the periphery. Consistent with this, iNKT cells from different organs show distinct basal activation, proliferation and clonal expansion. Moreover, the iNKT cell TCR repertoire changes following immunisation and is shaped by age and environmental changes. Thus, post-thymic modification of the TCR-repertoire underpins the distinct antigen specificity for iNKT cells in peripheral tissues
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Affiliation(s)
- Rebeca Jimeno
- The Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom
| | - Marta Lebrusant-Fernandez
- The Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom
| | - Christian Margreitter
- Randall Centre for Cell & Molecular Biophysics, King's College London, London, United Kingdom
| | - Beth Lucas
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Natacha Veerapen
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Gavin Kelly
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Franca Fraternali
- Randall Centre for Cell & Molecular Biophysics, King's College London, London, United Kingdom
| | - Jo Spencer
- The Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Graham Anderson
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Patricia Barral
- The Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom
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Young J, Dominicus C, Wagener J, Butterworth S, Ye X, Kelly G, Ordan M, Saunders B, Instrell R, Howell M, Stewart A, Treeck M. A CRISPR platform for targeted in vivo screens identifies Toxoplasma gondii virulence factors in mice. Nat Commun 2019; 10:3963. [PMID: 31481656 PMCID: PMC6722137 DOI: 10.1038/s41467-019-11855-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [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: 07/04/2019] [Accepted: 08/07/2019] [Indexed: 02/08/2023] Open
Abstract
Genome-wide CRISPR screening is a powerful tool to identify genes required under selective conditions. However, the inherent scale of genome-wide libraries can limit their application in experimental settings where cell numbers are restricted, such as in vivo infections or single cell analysis. The use of small scale CRISPR libraries targeting gene subsets circumvents this problem. Here we develop a method for rapid generation of custom guide RNA (gRNA) libraries using arrayed single-stranded oligonucleotides for reproducible pooled cloning of CRISPR/Cas9 libraries. We use this system to generate mutant pools of different sizes in the protozoan parasite Toxoplasma gondi and describe optimised analysis methods for small scale libraries. An in vivo genetic screen in the murine host identifies novel and known virulence factors and we confirm results using cloned knock-out parasites. Our study also reveals a potential trans-rescue of individual knock-out parasites in pools of mutants compared to homogenous knock-out lines of the key virulence factor MYR1.
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Affiliation(s)
- Joanna Young
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Caia Dominicus
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Jeanette Wagener
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Simon Butterworth
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Xingda Ye
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Merav Ordan
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Becky Saunders
- High Throughput Screening Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Rachael Instrell
- High Throughput Screening Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Michael Howell
- High Throughput Screening Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Aengus Stewart
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Moritz Treeck
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK.
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48
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Omenetti S, Bussi C, Metidji A, Iseppon A, Lee S, Tolaini M, Li Y, Kelly G, Chakravarty P, Shoaie S, Gutierrez MG, Stockinger B. The Intestine Harbors Functionally Distinct Homeostatic Tissue-Resident and Inflammatory Th17 Cells. Immunity 2019; 51:77-89.e6. [PMID: 31229354 PMCID: PMC6642154 DOI: 10.1016/j.immuni.2019.05.004] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [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: 10/02/2018] [Revised: 02/28/2019] [Accepted: 05/14/2019] [Indexed: 02/06/2023]
Abstract
T helper 17 (Th17) cells are pathogenic in many inflammatory diseases, but also support the integrity of the intestinal barrier in a non-inflammatory manner. It is unclear what distinguishes inflammatory Th17 cells elicited by pathogens and tissue-resident homeostatic Th17 cells elicited by commensals. Here, we compared the characteristics of Th17 cells differentiating in response to commensal bacteria (SFB) to those differentiating in response to a pathogen (Citrobacter rodentium). Homeostatic Th17 cells exhibited little plasticity towards expression of inflammatory cytokines, were characterized by a metabolism typical of quiescent or memory T cells, and did not participate in inflammatory processes. In contrast, infection-induced Th17 cells showed extensive plasticity towards pro-inflammatory cytokines, disseminated widely into the periphery, and engaged aerobic glycolysis in addition to oxidative phosphorylation typical for inflammatory effector cells. These findings will help ensure that future therapies directed against inflammatory Th17 cells do not inadvertently damage the resident gut population. Tissue-resident, SFB-elicited Th17 cells are non-inflammatory Citrobacter-elicited Th17 cells show high plasticity towards inflammatory cytokines SFB Th17 cells are metabolically similar to resting memory cells Citrobacter Th17 cells are highly glycolytic effector cells
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Affiliation(s)
- Sara Omenetti
- The Francis Crick Institute, 1 Midland Road London NW1 1AT, UK
| | - Claudio Bussi
- The Francis Crick Institute, 1 Midland Road London NW1 1AT, UK
| | - Amina Metidji
- The Francis Crick Institute, 1 Midland Road London NW1 1AT, UK; Present Address: Centre de Recherche scientifique et technique en Analyses Physico-Chimiques (C.R.A.P.C), Alger, Algérie
| | - Andrea Iseppon
- The Francis Crick Institute, 1 Midland Road London NW1 1AT, UK
| | - Sunjae Lee
- The Francis Crick Institute, 1 Midland Road London NW1 1AT, UK; Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, UK
| | - Mauro Tolaini
- The Francis Crick Institute, 1 Midland Road London NW1 1AT, UK
| | - Ying Li
- The Francis Crick Institute, 1 Midland Road London NW1 1AT, UK
| | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road London NW1 1AT, UK
| | | | - Saeed Shoaie
- The Francis Crick Institute, 1 Midland Road London NW1 1AT, UK; Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, UK
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Derham AM, O'Leary JM, Connolly SE, Schumacher J, Kelly G. Performance comparison of 159 Thoroughbred racehorses and matched cohorts before and after desmotomy of the interspinous ligament. Vet J 2019; 249:16-23. [PMID: 31239160 DOI: 10.1016/j.tvjl.2019.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 11/16/2022]
Abstract
Racehorses may perform poorly because of impinging dorsal spinous processes (DSPs) of the thoracolumbar vertebrae. No study has looked objectively at the long-term outcome of racehorses undergoing desmotomy of the interspinous ligament as a treatment for horses with poor performance caused by impinging DSPs. The aim of this study was to examine objectively, by using pre-operative and post-operative racing records, the effectiveness of desmotomy of the interspinous ligament (DISL) in improving the performance of racehorses with impinging DSPs. Medical records of all horses undergoing desmotomy of one or more interspinous ligaments at a referral equine hospital, between February 2015 and September 2016, were reviewed. The study was confined to Thoroughbred racehorses with sufficient historical information and racetrack data to allow their racing performances be compared to that of matched controls. Matched controls were of the same age, sex, and racing type and were trained at the same time by the same trainer as those undergoing desmotomy. The time to follow-up was at least 12 months. Of the 6545 horses presented for poor performance or lameness during the study period, 236 horses (3.6%) underwent desmotomy of one or more interspinous ligaments, and of these, 159 met the inclusion criteria. Horses undergoing desmotomy had significantly better improvement in racing performance than did matched controls. Eight horses developed unilateral neurogenic atrophy of epaxial musculature. DISL between impinging DSPs can improve the performance of racehorses experiencing from poor performance caused by pain resulting from the impinging processes.
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Affiliation(s)
- A M Derham
- University College Dublin, University Veterinary Hospital, UCD, Belfield, Dublin 4, Ireland.
| | - J M O'Leary
- University College Dublin, University Veterinary Hospital, UCD, Belfield, Dublin 4, Ireland
| | - S E Connolly
- MRC Biostatistics Unit, University of Cambridge, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK
| | - J Schumacher
- Department of Large Animal Clinical Sciences, University of Tennessee, Knoxville, TN 37996, USA
| | - G Kelly
- Fethard Equine Hospital, Tipperary, Ireland
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50
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Wallbank BA, Dominicus CS, Broncel M, Legrave N, Kelly G, MacRae JI, Staines HM, Treeck M. Characterisation of the Toxoplasma gondii tyrosine transporter and its phosphorylation by the calcium-dependent protein kinase 3. Mol Microbiol 2019; 111:1167-1181. [PMID: 30402958 PMCID: PMC6488386 DOI: 10.1111/mmi.14156] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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] [Accepted: 10/20/2018] [Indexed: 12/21/2022]
Abstract
Toxoplasma gondii parasites rapidly exit their host cell when exposed to calcium ionophores. Calcium-dependent protein kinase 3 (TgCDPK3) was previously identified as a key mediator in this process, as TgCDPK3 knockout (∆cdpk3) parasites fail to egress in a timely manner. Phosphoproteomic analysis comparing WT with ∆cdpk3 parasites revealed changes in the TgCDPK3-dependent phosphoproteome that included proteins important for regulating motility, but also metabolic enzymes, indicating that TgCDPK3 controls processes beyond egress. Here we have investigated a predicted direct target of TgCDPK3, ApiAT5-3, a putative transporter of the major facilitator superfamily, and show that it is rapidly phosphorylated at serine 56 after induction of calcium signalling. Conditional knockout of apiAT5-3 results in transcriptional upregulation of most ribosomal subunits, but no alternative transporters, and subsequent parasite death. Mutating the S56 to a non-phosphorylatable alanine leads to a fitness cost, suggesting that phosphorylation of this residue is beneficial, albeit not essential, for tyrosine import. Using a combination of metabolomics and heterologous expression, we confirmed a primary role in tyrosine import for ApiAT5-3. However, no significant differences in tyrosine import could be detected in phosphorylation site mutants showing that if tyrosine transport is affected by S56 phosphorylation, its regulatory role is subtle.
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Affiliation(s)
- Bethan A. Wallbank
- Signalling in Apicomplexan Parasites LaboratoryThe Francis Crick InstituteLondonUK
| | - Caia S. Dominicus
- Signalling in Apicomplexan Parasites LaboratoryThe Francis Crick InstituteLondonUK
| | - Malgorzata Broncel
- Signalling in Apicomplexan Parasites LaboratoryThe Francis Crick InstituteLondonUK
| | - Nathalie Legrave
- Metabolomics Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - Gavin Kelly
- Bioinformatics and Biostatistics STPFrancis Crick Institute1 Midland RoadLondon NW1 1ATUK
| | - James I. MacRae
- Metabolomics Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - Henry M. Staines
- Institute of Infection and ImmunitySt George’s, University of LondonLondonUK
| | - Moritz Treeck
- Signalling in Apicomplexan Parasites LaboratoryThe Francis Crick InstituteLondonUK
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