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McWhorter JK, Halloran PR, Roff G, Mumby PJ. Climate change impacts on mesophotic regions of the Great Barrier Reef. Proc Natl Acad Sci U S A 2024; 121:e2303336121. [PMID: 38588432 PMCID: PMC11032494 DOI: 10.1073/pnas.2303336121] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 02/28/2024] [Indexed: 04/10/2024] Open
Abstract
Climate change projections for coral reefs are founded exclusively on sea surface temperatures (SST). While SST projections are relevant for the shallowest reefs, neglecting ocean stratification overlooks the striking differences in temperature experienced by deeper reefs for all or part of the year. Density stratification creates a buoyancy barrier partitioning the upper and lower parts of the water column. Here, we mechanistically downscale climate models and quantify patterns of thermal stratification above mesophotic corals (depth 30 to 50 m) of the Great Barrier Reef (GBR). Stratification insulates many offshore regions of the GBR from heatwaves at the surface. However, this protection is lost once global average temperatures exceed ~3 °C above preindustrial, after which mesophotic temperatures surpass a recognized threshold of 30 °C for coral mortality. Bottom temperatures on the GBR (30 to 50 m) from 2050 to 2060 are estimated to increase by ~0.5 to 1 °C under lower climate emissions (SSP1-1.9) and ~1.2 to 1.7 °C under higher climate emissions (SSP5-8.5). In short, mesophotic coral reefs are also threatened by climate change and research might prioritize the sensitivity of such corals to stress.
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Affiliation(s)
- Jennifer K. McWhorter
- Faculty of Environment, Science and Economy, University of Exeter, ExeterEX4 4QJ, United Kingdom
- Marine Spatial Ecology Lab, School of the Environment The University of Queensland, St Lucia, QLD4072, Australia
- National Oceanic and Atmospheric Administration, Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystem Divisions, Miami, FL33149
| | - Paul R. Halloran
- Faculty of Environment, Science and Economy, University of Exeter, ExeterEX4 4QJ, United Kingdom
| | - George Roff
- Marine Spatial Ecology Lab, School of the Environment The University of Queensland, St Lucia, QLD4072, Australia
- Commonwealth Scientific and Industrial Research Organisation, Oceans & Atmosphere, St Lucia, QLD 4000, Australia
| | - Peter J. Mumby
- Marine Spatial Ecology Lab, School of the Environment The University of Queensland, St Lucia, QLD4072, Australia
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2
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Geher-Herczegh T, Wang Z, Masuda T, Vasudevan N, Yoshida R, Hayashi Y. Harmonic resonance and entrainment of propagating chemical waves by external mechanical stimulation in BZ self-oscillating hydrogels. Proc Natl Acad Sci U S A 2024; 121:e2320331121. [PMID: 38593071 PMCID: PMC11032451 DOI: 10.1073/pnas.2320331121] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/20/2024] [Indexed: 04/11/2024] Open
Abstract
Smart polymer materials that are nonliving yet exhibit complex "life-like" or biomimetic behaviors have been the focus of intensive research over the past decades, in the quest to broaden our understanding of how living systems function under nonequilibrium conditions. Identification of how chemical and mechanical coupling can generate resonance and entrainment with other cells or external environment is an important research question. We prepared Belousov-Zhabotinsky (BZ) self-oscillating hydrogels which convert chemical energy to mechanical oscillation. By cyclically applying external mechanical stimulation to the BZ hydrogels, we found that when the oscillation of a gel sample entered into harmonic resonance with the applied oscillation during stimulation, the system kept a "memory" of the resonant oscillation period and maintained it post stimulation, demonstrating an entrainment effect. More surprisingly, by systematically varying the cycle length of the external stimulation, we revealed the discrete nature of the stimulation-induced resonance and entrainment behaviors in chemical oscillations of BZ hydrogels, i.e., the hydrogels slow down their oscillation periods to the harmonics of the cycle length of the external mechanical stimulation. Our theoretical model calculations suggest the important roles of the delayed mechanical response caused by reactant diffusion and solvent migration in affecting the chemomechanical coupling in active hydrogels and consequently synchronizing their chemical oscillations with external mechanical oscillations.
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Affiliation(s)
- Tunde Geher-Herczegh
- Department of Biomedical Sciences and Biomedical Engineering, School of Biological Sciences, University of Reading, ReadingRG6 6AS, United Kingdom
| | - Zuowei Wang
- Department of Mathematics and Statistics, School of Mathematical, Physical and Computational Sciences, University of Reading, ReadingRG6 6AX, United Kingdom
| | - Tsukuru Masuda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo113-8656, Japan
| | - Nandini Vasudevan
- Department of Biomedical Sciences and Biomedical Engineering, School of Biological Sciences, University of Reading, ReadingRG6 6AS, United Kingdom
| | - Ryo Yoshida
- Department of Materials Engineering, School of Engineering, The University of Tokyo, Tokyo113-8656, Japan
| | - Yoshikatsu Hayashi
- Department of Biomedical Sciences and Biomedical Engineering, School of Biological Sciences, University of Reading, ReadingRG6 6AS, United Kingdom
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3
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Goatley LC, Freimanis GL, Tennakoon C, Bastos A, Heath L, Netherton CL. African swine fever virus NAM P1/95 is a mixture of genotype I and genotype VIII viruses. Microbiol Resour Announc 2024; 13:e0006724. [PMID: 38526091 PMCID: PMC11008121 DOI: 10.1128/mra.00067-24] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/12/2024] [Indexed: 03/26/2024] Open
Abstract
African swine fever virus causes a lethal hemorrhagic disease of domestic pigs. The NAM P1/1995 isolate was originally described as B646L genotype XVIII; however, full genome sequencing revealed that this assignment was incorrect.
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Affiliation(s)
| | | | | | - Armanda Bastos
- Department of Zoology & Entomology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Livio Heath
- Agricultural Research Council-Onderstepoort Veterinary Institute, Onderstepoort, South Africa
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Alodaini D, Hernandez-Rocamora V, Boelter G, Ma X, Alao MB, Doherty HM, Bryant JA, Moynihan P, Moradigaravand D, Glinkowska M, Vollmer W, Banzhaf M. Reduced peptidoglycan synthesis capacity impairs growth of E. coli at high salt concentration. mBio 2024; 15:e0032524. [PMID: 38426748 PMCID: PMC11005333 DOI: 10.1128/mbio.00325-24] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
Gram-negative bacteria have a thin peptidoglycan layer between the cytoplasmic and outer membranes protecting the cell from osmotic challenges. Hydrolases of this structure are needed to cleave bonds to allow the newly synthesized peptidoglycan strands to be inserted by synthases. These enzymes need to be tightly regulated and their activities coordinated to prevent cell lysis. To better understand this process in Escherichia coli, we probed the genetic interactions of mrcA (encodes PBP1A) and mrcB (encodes PBP1B) with genes encoding peptidoglycan amidases and endopeptidases in envelope stress conditions. Our extensive genetic interaction network analysis revealed relatively few combinations of hydrolase gene deletions with reduced fitness in the absence of PBP1A or PBP1B, showing that none of the amidases or endopeptidases is strictly required for the functioning of one of the class A PBPs. This illustrates the robustness of the peptidoglycan growth mechanism. However, we discovered that the fitness of ∆mrcB cells is significantly reduced under high salt stress and in vitro activity assays suggest that this phenotype is caused by a reduced peptidoglycan synthesis activity of PBP1A at high salt concentration.IMPORTANCEEscherichia coli and many other bacteria have a surprisingly high number of peptidoglycan hydrolases. These enzymes function in concert with synthases to facilitate the expansion of the peptidoglycan sacculus under a range of growth and stress conditions. The synthases PBP1A and PBP1B both contribute to peptidoglycan expansion during cell division and growth. Our genetic interaction analysis revealed that these two penicillin-binding proteins (PBPs) do not need specific amidases, endopeptidases, or lytic transglycosylases for function. We show that PBP1A and PBP1B do not work equally well when cells encounter high salt stress and demonstrate that PBP1A alone cannot provide sufficient PG synthesis activity under this condition. These results show how the two class A PBPs and peptidoglycan hydrolases govern cell envelope integrity in E. coli in response to environmental challenges and particularly highlight the importance of PBP1B in maintaining cell fitness under high salt conditions.
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Affiliation(s)
- Dema Alodaini
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Victor Hernandez-Rocamora
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Gabriela Boelter
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Xuyu Ma
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Micheal B. Alao
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Hannah M. Doherty
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Jack A. Bryant
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Patrick Moynihan
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Danesh Moradigaravand
- KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Makkah, Saudi Arabia
- Laboratory for Infectious Disease Epidemiology, KAUST Smart-Health Initiative and Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, Saudi Arabia
| | - Monika Glinkowska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Waldemar Vollmer
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Manuel Banzhaf
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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5
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Francis VI, Liddle C, Camacho E, Kulkarni M, Junior SRS, Harvey JA, Ballou ER, Thomson DD, Brown GD, Hardwick JM, Casadevall A, Witton J, Coelho C. Cryptococcus neoformans rapidly invades the murine brain by sequential breaching of airway and endothelial tissues barriers, followed by engulfment by microglia. mBio 2024; 15:e0307823. [PMID: 38511961 PMCID: PMC11005363 DOI: 10.1128/mbio.03078-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
Cryptococcus neoformans causes lethal meningitis and accounts for approximately 10%-15% of AIDS-associated deaths worldwide. There are major gaps in our understanding of how this fungus invades the mammalian brain. To investigate the dynamics of C. neoformans tissue invasion, we mapped fungal localization and host cell interactions in infected brain, lung, and upper airways using mouse models of systemic and airway infection. To enable this, we developed an in situ imaging pipeline capable of measuring large volumes of tissue while preserving anatomical and cellular information by combining thick tissue sections, tissue clarification, and confocal imaging. We confirm high fungal burden in mouse upper airway after nasal inoculation. Yeast in turbinates were frequently titan cells, with faster kinetics than reported in mouse lungs. Importantly, we observed one instance of fungal cells enmeshed in lamina propria of the upper airways, suggesting penetration of airway mucosa as a possible route of tissue invasion and dissemination to the bloodstream. We extend previous literature positing bloodstream dissemination of C. neoformans, by finding viable fungi in the bloodstream of mice a few days after intranasal infection. As early as 24 h post systemic infection, the majority of C. neoformans cells traversed the blood-brain barrier, and were engulfed or in close proximity to microglia. Our work presents a new method for investigating microbial invasion, establishes that C. neoformans can breach multiple tissue barriers within the first days of infection, and demonstrates microglia as the first cells responding to C. neoformans invasion of the brain.IMPORTANCECryptococcal meningitis causes 10%-15% of AIDS-associated deaths globally. Still, brain-specific immunity to cryptococci is a conundrum. By employing innovative imaging, this study reveals what occurs during the first days of infection in brain and in airways. We found that titan cells predominate in upper airways and that cryptococci breach the upper airway mucosa, which implies that, at least in mice, the upper airways are a site for fungal dissemination. This would signify that mucosal immunity of the upper airway needs to be better understood. Importantly, we also show that microglia, the brain-resident macrophages, are the first responders to infection, and microglia clusters are formed surrounding cryptococci. This study opens the field to detailed molecular investigations on airway immune response, how fungus traverses the blood-brain barrier, how microglia respond to infection, and ultimately how microglia monitor the blood-brain barrier to preserve brain function.
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Affiliation(s)
- Vanessa I. Francis
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Corin Liddle
- Bioimaging Facility, University of Exeter, Exeter, United Kingdom
| | - Emma Camacho
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Madhura Kulkarni
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Jamie A. Harvey
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
| | - Elizabeth R. Ballou
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
| | - Darren D. Thomson
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
| | - Gordon D. Brown
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - J. Marie Hardwick
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Arturo Casadevall
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jonathan Witton
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Carolina Coelho
- MRC Centre for Medical Mycology at University of Exeter, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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6
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Polat C, Ayhan N, Ergünay K, Charrel RN. Comprehensive evaluation of nucleic acid amplification methods widely used for generic detection of sandfly-borne phleboviruses. Microbiol Spectr 2024; 12:e0342823. [PMID: 38456695 DOI: 10.1128/spectrum.03428-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/13/2024] [Indexed: 03/09/2024] Open
Abstract
Sandfly-borne phleboviruses (SBPs), which cause sandfly fever, aseptic meningitis, encephalitis, and meningoencephalitis, are emerging pathogens of major public health concern. Virus nucleic acid testing is essential for SBP diagnosis, especially in the early stages of infection, and for the discovery of novel SBPs. The efficacy of utilizing generic primers that target conserved nucleotide sequences for the detection of both known and novel SBPs has not been extensively evaluated. We aimed to compare and evaluate the performance of five generic primer sets, widely used to detect S- and L-segments of arthropod-borne phleboviruses and designed as singleplex (n = 3) and nested (n = 2) formats, including both well-known and recently characterized 15 Old World virus strains. Furthermore, we performed in silico analysis to assess the detection capabilities of these generic primer sets. The initial evaluation of previously published generic primer sets for SBP detection yielded two singleplex primer sets with the potential to be adapted for use in real-time or high-throughput detection settings. Studies are ongoing to develop and further optimize a preliminary assay and test various hosts and vectors to assess their capacity to detect known and novel viruses. IMPORTANCE Virus nucleic acid testing is the primary diagnostic method, particularly in the early stages of illness. Virus-specific or syndromic tests are widely used for this purpose. The use of generic primers has had a considerable impact on the discovery, identification, and detection of Old World sandfly-borne phleboviruses (OWSBP). The study is significant because it is the first to carry out a comparative evaluation of all published OWSBP generic primer sets.
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Affiliation(s)
- Ceylan Polat
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
- Unité des Virus Emergents, Aix Marseille University, Marseille, France
| | - Nazli Ayhan
- Unité des Virus Emergents, Aix Marseille University, Marseille, France
- National Reference Center for Arboviruses, National Institute of Health, and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Koray Ergünay
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, Maryland, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, Maryland, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History (NMNH), Washington, DC, USA
| | - Remi N Charrel
- Unité des Virus Emergents, Aix Marseille University, Marseille, France
- Laboratoire des Infections Virales Aigues et Tropicales, Pole des Maladies Infectieuses, AP-HM Hopitaux Universitaires de Marseille, Marseille, France
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7
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Boston RH, Guan R, Kalmar L, Beier S, Horner EC, Beristain-Covarrubias N, Yam-Puc JC, Pereyra Gerber P, Faria L, Kuroshchenkova A, Lindell AE, Blasche S, Correa-Noguera A, Elmer A, Saunders C, Bermperi A, Jose S, Kingston N, Grigoriadou S, Staples E, Buckland MS, Lear S, Matheson NJ, Benes V, Parkinson C, Thaventhiran JE, Patil KR. Stability of gut microbiome after COVID-19 vaccination in healthy and immuno-compromised individuals. Life Sci Alliance 2024; 7:e202302529. [PMID: 38316462 PMCID: PMC10844540 DOI: 10.26508/lsa.202302529] [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: 12/13/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 02/07/2024] Open
Abstract
Bidirectional interactions between the immune system and the gut microbiota are key contributors to various physiological functions. Immune-associated diseases such as cancer and autoimmunity, and efficacy of immunomodulatory therapies, have been linked to microbiome variation. Although COVID-19 infection has been shown to cause microbial dysbiosis, it remains understudied whether the inflammatory response associated with vaccination also impacts the microbiota. Here, we investigate the temporal impact of COVID-19 vaccination on the gut microbiome in healthy and immuno-compromised individuals; the latter included patients with primary immunodeficiency and cancer patients on immunomodulating therapies. We find that the gut microbiome remained remarkably stable post-vaccination irrespective of diverse immune status, vaccine response, and microbial composition spanned by the cohort. The stability is evident at all evaluated levels including diversity, phylum, species, and functional capacity. Our results indicate the resilience of the gut microbiome to host immune changes triggered by COVID-19 vaccination and suggest minimal, if any, impact on microbiome-mediated processes. These findings encourage vaccine acceptance, particularly when contrasted with the significant microbiome shifts observed during COVID-19 infection.
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Affiliation(s)
- Rebecca H Boston
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Rui Guan
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Lajos Kalmar
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Sina Beier
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Emily C Horner
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Juan Carlos Yam-Puc
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Pehuén Pereyra Gerber
- https://ror.org/013meh722 Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- https://ror.org/013meh722 Department of Medicine, University of Cambridge, Cambridge, UK
| | - Luisa Faria
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Anna Kuroshchenkova
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Anna E Lindell
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Sonja Blasche
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Andrea Correa-Noguera
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Anne Elmer
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | | | - Areti Bermperi
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - Sherly Jose
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Emily Staples
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Matthew S Buckland
- Department of Clinical Immunology, Barts Health, London, UK
- UCL GOSH Institute of Child Health Division of Infection and Immunity, Section of Cellular and Molecular Immunology, London, UK
| | - Sara Lear
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Nicholas J Matheson
- https://ror.org/013meh722 Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- https://ror.org/013meh722 Department of Medicine, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Vladimir Benes
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christine Parkinson
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - James Ed Thaventhiran
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
- Department of Clinical Immunology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Kiran R Patil
- https://ror.org/013meh722 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
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Costa TFR, Catta-Preta CMC, Goundry A, Carvalho DB, Rodrigues NS, Vivarini AC, de Abreu MF, Reis FCG, Lima APCA. The ecotin-like peptidase inhibitor of Trypanosoma cruzi prevents TMPRSS2-PAR2-TLR4 crosstalk downmodulating infection and inflammation. FASEB J 2024; 38:e23566. [PMID: 38526868 DOI: 10.1096/fj.202302091rr] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 02/24/2024] [Accepted: 03/06/2024] [Indexed: 03/27/2024]
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, a chronic pathology that affects the heart and/or digestive system. This parasite invades and multiplies in virtually all nucleated cells, using a variety of host cell receptors for infection. T. cruzi has a gene that encodes an ecotin-like inhibitor of serine peptidases, ISP2. We generated ISP2-null mutants (Δisp2) in T. cruzi Dm28c using CRISPR/Cas9. Epimastigotes of Δisp2 grew normally in vitro but were more susceptible to lysis by human serum compared to parental and ISP2 add-back lines. Tissue culture trypomastigotes of Δisp2 were more infective to human muscle cells in vitro, which was reverted by the serine peptidase inhibitors aprotinin and camostat, suggesting that host cell epitheliasin/TMPRSS2 is the target of ISP2. Pretreatment of host cells with an antagonist to the protease-activated receptor 2 (PAR2) or an inhibitor of Toll-like receptor 4 (TLR4) selectively counteracted the increased cell invasion by Δisp2, but did not affect invasion by parental and add-back lines. The same was observed following targeted gene silencing of PAR2, TLR4 or TMPRSS2 in host cells by siRNA. Furthermore, Δisp2 caused increased tissue edema in a BALB/c mouse footpad infection model after 3 h differently to that observed following infection with parental and add-back lines. We propose that ISP2 contributes to protect T. cruzi from the anti-microbial effects of human serum and to prevent triggering of PAR2 and TLR4 in host cells, resulting in the modulation of host cell invasion and contributing to decrease inflammation during acute infection.
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Affiliation(s)
- Tatiana F R Costa
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carolina M C Catta-Preta
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amy Goundry
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Danielle B Carvalho
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nathalia S Rodrigues
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Aislan C Vivarini
- Departamento de Biologia Celular e Molecular, Insituto de Biologia, Universidade Federal Fluminense, Niteroi, Brazil
| | - Mayra Fonseca de Abreu
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Flavia C G Reis
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Paula C A Lima
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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9
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Nev OA, Duvenage L, Brown AJP, Dangarembizi R, Hoving JC. Slicing through the challenge of maintaining Pneumocystis in the laboratory. mBio 2024; 15:e0327723. [PMID: 38345378 PMCID: PMC10936409 DOI: 10.1128/mbio.03277-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Abstract
Pneumocystis jirovecii is a major fungal pathogen of humans that causes life-threatening lung infections in immunocompromised individuals. Despite its huge global impact upon human health, our understanding of the pathobiology of this deadly fungus remains extremely limited, largely because it is not yet possible to cultivate Pneumocystis in vitro, independently of the host. However, a recent paper by Munyonho et al. offers a major step forward (F. T. Munyonho, R. D. Clark, D. Lin, M. S. Khatun, et al., 2023, mBio 15:e01464-23, https://doi.org/10.1128/mbio.01464-23). They show that it is possible to maintain both the trophozoite and cyst forms of the mouse pathogen, Pneumocystis murina, in precision-cut lung slices for several weeks. Furthermore, they demonstrate that this offers the exciting opportunity to examine potential virulence factors such as possible biofilm formation as well as antifungal drug responses in the lung.
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Affiliation(s)
- Olga A. Nev
- Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Lucian Duvenage
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
- CMM AFRICA Medical Mycology Research Unit, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Pathology, Division of Immunology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Alistair J. P. Brown
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Rachael Dangarembizi
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
- CMM AFRICA Medical Mycology Research Unit, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Human Biology, Division of Physiological Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Jennifer Claire Hoving
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
- CMM AFRICA Medical Mycology Research Unit, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Pathology, Division of Immunology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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10
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De Strooper B, Karran E. New precision medicine avenues to the prevention of Alzheimer's disease from insights into the structure and function of γ-secretases. EMBO J 2024; 43:887-903. [PMID: 38396302 PMCID: PMC10943082 DOI: 10.1038/s44318-024-00057-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/20/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Two phase-III clinical trials with anti-amyloid peptide antibodies have met their primary goal, i.e. slowing of Alzheimer's disease (AD) progression. However, antibody therapy may not be the optimal therapeutic modality for AD prevention, as we will discuss in the context of the earlier small molecules described as "γ-secretase modulators" (GSM). We review here the structure, function, and pathobiology of γ-secretases, with a focus on how mutations in presenilin genes result in early-onset AD. Significant progress has been made in generating compounds that act in a manner opposite to pathogenic presenilin mutations: they stabilize the proteinase-substrate complex, thereby increasing the processivity of substrate cleavage and altering the size spectrum of Aβ peptides produced. We propose the term "γ-secretase allosteric stabilizers" (GSAS) to distinguish these compounds from the rather heterogenous class of GSM. The GSAS represent, in theory, a precision medicine approach to the prevention of amyloid deposition, as they specifically target a discrete aspect in a complex cell biological signalling mechanism that initiates the pathological processes leading to Alzheimer's disease.
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Affiliation(s)
- Bart De Strooper
- Dementia Research Institute, Institute of Neurology, University College London, at the Francis Crick Institute, London, NW1 AT, UK.
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, and Leuven Brain Institute, KU Leuven, Leuven, 3000, Belgium.
| | - Eric Karran
- Cambridge Research Center, AbbVie, Inc., Cambridge, MA, USA
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11
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Bandau S, Alvarez V, Jiang H, Graff S, Sundaramoorthy R, Gierlinski M, Toman M, Owen-Hughes T, Sidoli S, Lamond A, Alabert C. RNA polymerase II promotes the organization of chromatin following DNA replication. EMBO Rep 2024; 25:1387-1414. [PMID: 38347224 PMCID: PMC10933433 DOI: 10.1038/s44319-024-00085-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/18/2024] Open
Abstract
Understanding how chromatin organisation is duplicated on the two daughter strands is a central question in epigenetics. In mammals, following the passage of the replisome, nucleosomes lose their defined positioning and transcription contributes to their re-organisation. However, whether transcription plays a greater role in the organization of chromatin following DNA replication remains unclear. Here we analysed protein re-association with newly replicated DNA upon inhibition of transcription using iPOND coupled to quantitative mass spectrometry. We show that nucleosome assembly and the re-establishment of most histone modifications are uncoupled from transcription. However, RNAPII acts to promote the re-association of hundreds of proteins with newly replicated chromatin via pathways that are not observed in steady-state chromatin. These include ATP-dependent remodellers, transcription factors and histone methyltransferases. We also identify a set of DNA repair factors that may handle transcription-replication conflicts during normal transcription in human non-transformed cells. Our study reveals that transcription plays a greater role in the organization of chromatin post-replication than previously anticipated.
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Affiliation(s)
- Susanne Bandau
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Vanesa Alvarez
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Hao Jiang
- Laboratory of Quantitative Proteomics, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Sarah Graff
- Department of Biochemistry at the Albert Einstein College of Medicine, New York, NY, USA
| | | | - Marek Gierlinski
- Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Matt Toman
- Laboratory of Chromatin Structure and Function, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Tom Owen-Hughes
- Laboratory of Chromatin Structure and Function, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Simone Sidoli
- Department of Biochemistry at the Albert Einstein College of Medicine, New York, NY, USA
| | - Angus Lamond
- Laboratory of Quantitative Proteomics, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Constance Alabert
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK.
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12
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Beerling DJ, Epihov DZ, Kantola IB, Masters MD, Reershemius T, Planavsky NJ, Reinhard CT, Jordan JS, Thorne SJ, Weber J, Val Martin M, Freckleton RP, Hartley SE, James RH, Pearce CR, DeLucia EH, Banwart SA. Enhanced weathering in the US Corn Belt delivers carbon removal with agronomic benefits. Proc Natl Acad Sci U S A 2024; 121:e2319436121. [PMID: 38386712 PMCID: PMC10907306 DOI: 10.1073/pnas.2319436121] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/30/2023] [Indexed: 02/24/2024] Open
Abstract
Terrestrial enhanced weathering (EW) of silicate rocks, such as crushed basalt, on farmlands is a promising scalable atmospheric carbon dioxide removal (CDR) strategy that urgently requires performance assessment with commercial farming practices. We report findings from a large-scale replicated EW field trial across a typical maize-soybean rotation on an experimental farm in the heart of the United Sates Corn Belt over 4 y (2016 to 2020). We show an average combined loss of major cations (Ca2+ and Mg2+) from crushed basalt applied each fall over 4 y (50 t ha-1 y-1) gave a conservative time-integrated cumulative CDR potential of 10.5 ± 3.8 t CO2 ha-1. Maize and soybean yields increased significantly (P < 0.05) by 12 to 16% with EW following improved soil fertility, decreased soil acidification, and upregulation of root nutrient transport genes. Yield enhancements with EW were achieved with significantly (P < 0.05) increased key micro- and macronutrient concentrations (including potassium, magnesium, manganese, phosphorus, and zinc), thus improving or maintaining crop nutritional status. We observed no significant increase in the content of trace metals in grains of maize or soybean or soil exchangeable pools relative to controls. Our findings suggest that widespread adoption of EW across farming sectors has the potential to contribute significantly to net-zero greenhouse gas emissions goals while simultaneously improving food and soil security.
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Affiliation(s)
- David J. Beerling
- Leverhulme Centre for Climate Change Mitigation, School of Biosciences, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Dimitar Z. Epihov
- Leverhulme Centre for Climate Change Mitigation, School of Biosciences, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Ilsa B. Kantola
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Michael D. Masters
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Tom Reershemius
- Yale Center for Natural Carbon Capture, Department of Earth & Planetary Sciences, Yale University, New Haven, CT 06511
| | - Noah J. Planavsky
- Yale Center for Natural Carbon Capture, Department of Earth & Planetary Sciences, Yale University, New Haven, CT 06511
| | - Christopher T. Reinhard
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | | | - Sarah J. Thorne
- Leverhulme Centre for Climate Change Mitigation, School of Biosciences, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - James Weber
- Leverhulme Centre for Climate Change Mitigation, School of Biosciences, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Maria Val Martin
- Leverhulme Centre for Climate Change Mitigation, School of Biosciences, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Robert P. Freckleton
- Leverhulme Centre for Climate Change Mitigation, School of Biosciences, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Sue E. Hartley
- Leverhulme Centre for Climate Change Mitigation, School of Biosciences, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Rachael H. James
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, SouthamptonSO14 3ZH, United Kingdom
| | | | - Evan H. DeLucia
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Steven A. Banwart
- Global Food and Environment Institute, University of Leeds, LeedsLS2 9JT, United Kingdom
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, United Kingdom
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13
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Hilton J, Nanao Y, Flokstra M, Askari M, Smith TK, Di Falco A, King PDC, Wahl P, Adamson CS. The role of ion dissolution in metal and metal oxide surface inactivation of SARS-CoV-2. Appl Environ Microbiol 2024; 90:e0155323. [PMID: 38259079 PMCID: PMC10880620 DOI: 10.1128/aem.01553-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/28/2023] [Indexed: 01/24/2024] Open
Abstract
Anti-viral surface coatings are under development to prevent viral fomite transmission from high-traffic touch surfaces in public spaces. Copper's anti-viral properties have been widely documented, but the anti-viral mechanism of copper surfaces is not fully understood. We screened a series of metal and metal oxide surfaces for anti-viral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19). Copper and copper oxide surfaces exhibited superior anti-SARS-CoV-2 activity; however, the level of anti-viral activity was dependent on the composition of the carrier solution used to deliver virus inoculum. We demonstrate that copper ions released into solution from test surfaces can mediate virus inactivation, indicating a copper ion dissolution-dependent anti-viral mechanism. The level of anti-viral activity is, however, not dependent on the amount of copper ions released into solution per se. Instead, our findings suggest that degree of virus inactivation is dependent on copper ion complexation with other biomolecules (e.g., proteins/metabolites) in the virus carrier solution that compete with viral components. Although using tissue culture-derived virus inoculum is experimentally convenient to evaluate the anti-viral activity of copper-derived test surfaces, we propose that the high organic content of tissue culture medium reduces the availability of "uncomplexed" copper ions to interact with the virus, negatively affecting virus inactivation and hence surface anti-viral performance. We propose that laboratory anti-viral surface testing should include virus delivered in a physiologically relevant carrier solution (saliva or nasal secretions when testing respiratory viruses) to accurately predict real-life surface anti-viral performance when deployed in public spaces.IMPORTANCEThe purpose of evaluating the anti-viral activity of test surfaces in the laboratory is to identify surfaces that will perform efficiently in preventing fomite transmission when deployed on high-traffic touch surfaces in public spaces. The conventional method in laboratory testing is to use tissue culture-derived virus inoculum; however, this study demonstrates that anti-viral performance of test copper-containing surfaces is dependent on the composition of the carrier solution in which the virus inoculum is delivered to test surfaces. Therefore, we recommend that laboratory surface testing should include virus delivered in a physiologically relevant carrier solution to accurately predict real-life test surface performance in public spaces. Understanding the mechanism of virus inactivation is key to future rational design of improved anti-viral surfaces. Here, we demonstrate that release of copper ions from copper surfaces into small liquid droplets containing SARS-CoV-2 is a mechanism by which the virus that causes COVID-19 can be inactivated.
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Affiliation(s)
- Jane Hilton
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Yoshiko Nanao
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Machiel Flokstra
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Meisam Askari
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Terry K. Smith
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Andrea Di Falco
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Phil D. C. King
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Peter Wahl
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Catherine S. Adamson
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
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14
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Pearce D, Brooks E, Wright C, Rankin D, Crombie AT, Murrell JC. Complete genome sequences of Methylococcus capsulatus (Norfolk) and Methylocaldum szegediense (Norfolk) isolated from a landfill methane biofilter. Microbiol Resour Announc 2024; 13:e0067523. [PMID: 38236040 PMCID: PMC10868220 DOI: 10.1128/mra.00675-23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 12/10/2023] [Indexed: 01/19/2024] Open
Abstract
Here we report the complete genome sequence of two moderately thermophilic methanotrophs isolated from a landfill methane biofilter, Methylococcus capsulatus (Norfolk) and Methylocaldum szegediense (Norfolk).
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Affiliation(s)
- David Pearce
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Elliot Brooks
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | | | | | - Andrew T. Crombie
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
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15
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Farrington N, Dubey V, Johnson A, Horner I, Stevenson A, Unsworth J, Jimenez-Valverde A, Schwartz J, Das S, Hope W, Darlow CA. Molecular pharmacodynamics of meropenem for nosocomial pneumonia caused by Pseudomonas aeruginosa. mBio 2024; 15:e0316523. [PMID: 38236031 PMCID: PMC10865990 DOI: 10.1128/mbio.03165-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Hospital-acquired pneumonia (HAP) is a leading cause of morbidity and mortality, commonly caused by Pseudomonas aeruginosa. Meropenem is a commonly used therapeutic agent, although emergent resistance occurs during treatment. We used a rabbit HAP infection model to assess the bacterial kill and resistance pharmacodynamics of meropenem. Meropenem 5 mg/kg administered subcutaneously (s.c.) q8h (±amikacin 3.33-5 mg/kg q8h administered intravenously[i.v.]) or meropenem 30 mg/kg s.c. q8h regimens were assessed in a rabbit lung infection model infected with P. aeruginosa, with bacterial quantification and phenotypic/genotypic characterization of emergent resistant isolates. The pharmacokinetic/pharmacodynamic output was fitted to a mathematical model, and human-like regimens were simulated to predict outcomes in a clinical context. Increasing meropenem monotherapy demonstrated a dose-response effect to bacterial kill and an inverted U relationship with emergent resistance. The addition of amikacin to meropenem suppressed the emergence of resistance. A network of porin loss, efflux upregulation, and increased expression of AmpC was identified as the mechanism of this emergent resistance. A bridging simulation using human pharmacokinetics identified meropenem 2 g i.v. q8h as the licensed clinical regimen most likely to suppress resistance. We demonstrate an innovative experimental platform to phenotypically and genotypically characterize bacterial emergent resistance pharmacodynamics in HAP. For meropenem, we have demonstrated the risk of resistance emergence during therapy and identified two mitigating strategies: (i) regimen intensification and (ii) use of combination therapy. This platform will allow pre-clinical assessment of emergent resistance risk during treatment of HAP for other antimicrobials, to allow construction of clinical regimens that mitigate this risk.IMPORTANCEThe emergence of antimicrobial resistance (AMR) during antimicrobial treatment for hospital-acquired pneumonia (HAP) is a well-documented problem (particularly in pneumonia caused by Pseudomonas aeruginosa) that contributes to the wider global antimicrobial resistance crisis. During drug development, regimens are typically determined by their sufficiency to achieve bactericidal effect. Prevention of the emergence of resistance pharmacodynamics is usually not characterized or used to determine the regimen. The innovative experimental platform described here allows characterization of the emergence of AMR during the treatment of HAP and the development of strategies to mitigate this. We have demonstrated this specifically for meropenem-a broad-spectrum antibiotic commonly used to treat HAP. We have characterized the antimicrobial resistance pharmacodynamics of meropenem when used to treat HAP, caused by initially meropenem-susceptible P. aeruginosa, phenotypically and genotypically. We have also shown that intensifying the regimen and using combination therapy are both strategies that can both treat HAP and suppress the emergence of resistance.
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Affiliation(s)
- Nicola Farrington
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology, University of Liverpool, Liverpool Health Partners, Liverpool, United Kingdom
| | - Vineet Dubey
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology, University of Liverpool, Liverpool Health Partners, Liverpool, United Kingdom
| | - Adam Johnson
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology, University of Liverpool, Liverpool Health Partners, Liverpool, United Kingdom
| | - Iona Horner
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology, University of Liverpool, Liverpool Health Partners, Liverpool, United Kingdom
| | - Adam Stevenson
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology, University of Liverpool, Liverpool Health Partners, Liverpool, United Kingdom
| | - Jennifer Unsworth
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology, University of Liverpool, Liverpool Health Partners, Liverpool, United Kingdom
| | - Ana Jimenez-Valverde
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology, University of Liverpool, Liverpool Health Partners, Liverpool, United Kingdom
| | | | - Shampa Das
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology, University of Liverpool, Liverpool Health Partners, Liverpool, United Kingdom
| | - William Hope
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology, University of Liverpool, Liverpool Health Partners, Liverpool, United Kingdom
| | - Christopher A. Darlow
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology, University of Liverpool, Liverpool Health Partners, Liverpool, United Kingdom
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16
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Röntgen A, Toprakcioglu Z, Tomkins JE, Vendruscolo M. Modulation of α-synuclein in vitro aggregation kinetics by its alternative splice isoforms. Proc Natl Acad Sci U S A 2024; 121:e2313465121. [PMID: 38324572 PMCID: PMC10873642 DOI: 10.1073/pnas.2313465121] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/20/2023] [Indexed: 02/09/2024] Open
Abstract
The misfolding and aggregation of α-synuclein is linked to a family of neurodegenerative disorders known as synucleinopathies, the most prominent of which is Parkinson's disease (PD). Understanding the aggregation process of α-synuclein from a mechanistic point of view is thus of key importance. SNCA, the gene encoding α-synuclein, comprises six exons and produces various isoforms through alternative splicing. The most abundant isoform is expressed as a 140-amino acid protein (αSyn-140), while three other isoforms, αSyn-126, αSyn-112, and αSyn-98, are generated by skipping exon 3, exon 5, or both exons, respectively. In this study, we performed a detailed biophysical characterization of the aggregation of these four isoforms. We found that αSyn-112 and αSyn-98 exhibit accelerated aggregation kinetics compared to αSyn-140 and form distinct aggregate morphologies, as observed by transmission electron microscopy. Moreover, we observed that the presence of relatively small amounts of αSyn-112 accelerates the aggregation of αSyn-140, significantly reducing the aggregation half-time. These results indicate a potential role of alternative splicing in the pathological aggregation of α-synuclein and provide insights into how this process could be associated with the development of synucleinopathies.
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Affiliation(s)
- Alexander Röntgen
- Centre for Misfolding Diseases, Yusuf HamiedDepartment of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Zenon Toprakcioglu
- Centre for Misfolding Diseases, Yusuf HamiedDepartment of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - James E. Tomkins
- Centre for Misfolding Diseases, Yusuf HamiedDepartment of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf HamiedDepartment of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
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17
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McRae EKS, Wan CJK, Kristoffersen EL, Hansen K, Gianni E, Gallego I, Curran JF, Attwater J, Holliger P, Andersen ES. Cryo-EM structure and functional landscape of an RNA polymerase ribozyme. Proc Natl Acad Sci U S A 2024; 121:e2313332121. [PMID: 38207080 PMCID: PMC10801858 DOI: 10.1073/pnas.2313332121] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024] Open
Abstract
The emergence of an RNA replicase capable of self-replication is considered an important stage in the origin of life. RNA polymerase ribozymes (PR) - including a variant that uses trinucleotide triphosphates (triplets) as substrates - have been created by in vitro evolution and are the closest functional analogues of the replicase, but the structural basis for their function is poorly understood. Here we use single-particle cryogenic electron microscopy (cryo-EM) and high-throughput mutation analysis to obtain the structure of a triplet polymerase ribozyme (TPR) apoenzyme and map its functional landscape. The cryo-EM structure at 5-Å resolution reveals the TPR as an RNA heterodimer comprising a catalytic subunit and a noncatalytic, auxiliary subunit, resembling the shape of a left hand with thumb and fingers at a 70° angle. The two subunits are connected by two distinct kissing-loop (KL) interactions that are essential for polymerase function. Our combined structural and functional data suggest a model for templated RNA synthesis by the TPR holoenzyme, whereby heterodimer formation and KL interactions preorganize the TPR for optimal primer-template duplex binding, triplet substrate discrimination, and templated RNA synthesis. These results provide a better understanding of TPR structure and function and should aid the engineering of more efficient PRs.
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Affiliation(s)
- Ewan K. S. McRae
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Christopher J. K. Wan
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Emil L. Kristoffersen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Kalinka Hansen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
| | - Edoardo Gianni
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Isaac Gallego
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Joseph F. Curran
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - James Attwater
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Philipp Holliger
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Ebbe S. Andersen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
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18
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Williams AD, Rousham E, Neal AL, Amin MB, Hobman JL, Stekel D, Islam MA. Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh. Microbiol Spectr 2023; 11:e0176323. [PMID: 37971224 PMCID: PMC10714819 DOI: 10.1128/spectrum.01763-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/19/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Through the use of DNA sequencing, our study shows that there is no significant difference in the antibiotic resistance genes found in stool samples taken from individuals with high exposure to poultry routinely fed antibiotics and those without such exposure. This finding is significant as it suggests limited transmission of antibiotic resistance genes between poultry and humans in these circumstances. However, our research also demonstrates that commercially reared poultry are more likely to possess resistance genes to antibiotics commonly administered on medium-sized farms. Additionally, our study highlights the under-explored potential of wastewater as a source of various antibiotic resistance genes, some of which are clinically relevant.
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Affiliation(s)
- Alexander D. Williams
- Laboratory of Data Discovery for Health Ltd, Hong Kong Science and Technology Park, Tai Po, Hong Kong
- School of Public Health, University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Emily Rousham
- Centre for Global Health and Human Development, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, United Kingdom
| | - Andrew L. Neal
- Net-Zero and Resilient Farming, Rothamsted Research, North Wyke, United Kingdom
| | - Mohammed Badrul Amin
- Laboratory of Food Safety and One Health, Laboratory Sciences and Services Division, icddr,b, Dhaka, Bangladesh
| | - Jon L. Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, United Kingdom
| | - Dov Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, United Kingdom
- Department of Mathematics and Applied Mathematics, University of Johannesburg, Auckland Park, South Africa
| | - Mohammad Aminul Islam
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
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19
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Liu Q, Maqbool A, Mirkin FG, Singh Y, Stevenson CEM, Lawson DM, Kamoun S, Huang W, Hogenhout SA. Bimodular architecture of bacterial effector SAP05 that drives ubiquitin-independent targeted protein degradation. Proc Natl Acad Sci U S A 2023; 120:e2310664120. [PMID: 38039272 DOI: 10.1073/pnas.2310664120] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/19/2023] [Indexed: 12/03/2023] Open
Abstract
In eukaryotes, targeted protein degradation (TPD) typically depends on a series of interactions among ubiquitin ligases that transfer ubiquitin molecules to substrates leading to degradation by the 26S proteasome. We previously identified that the bacterial effector protein SAP05 mediates ubiquitin-independent TPD. SAP05 forms a ternary complex via interactions with the von Willebrand Factor Type A (vWA) domain of the proteasomal ubiquitin receptor Rpn10 and the zinc-finger (ZnF) domains of the SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) and GATA BINDING FACTOR (GATA) transcription factors (TFs). This leads to direct TPD of the TFs by the 26S proteasome. Here, we report the crystal structures of the SAP05-Rpn10vWA complex at 2.17 Å resolution and of the SAP05-SPL5ZnF complex at 2.20 Å resolution. Structural analyses revealed that SAP05 displays a remarkable bimodular architecture with two distinct nonoverlapping surfaces, a "loop surface" with three protruding loops that form electrostatic interactions with ZnF, and a "sheet surface" featuring two β-sheets, loops, and α-helices that establish polar interactions with vWA. SAP05 binding to ZnF TFs involves single amino acids responsible for multiple contacts, while SAP05 binding to vWA is more stable due to the necessity of multiple mutations to break the interaction. In addition, positioning of the SAP05 complex on the 26S proteasome points to a mechanism of protein degradation. Collectively, our findings demonstrate how a small bacterial bimodular protein can bypass the canonical ubiquitin-proteasome proteolysis pathway, enabling ubiquitin-independent TPD in eukaryotic cells. This knowledge holds significant potential for the creation of TPD technologies.
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Affiliation(s)
- Qun Liu
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Abbas Maqbool
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Federico G Mirkin
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Yeshveer Singh
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Clare E M Stevenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - David M Lawson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Weijie Huang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Centre for Plant Stress Biology, Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 20032, China
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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20
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Scott HR, Warran K, Fraser K, Chipp B, McGinnes G, Towers M, Lloyd-Evans B, Sheridan Rains L. A realist interview study of a participatory public mental health project "#KindnessByPost". BMC Public Health 2023; 23:2406. [PMID: 38049751 PMCID: PMC10694983 DOI: 10.1186/s12889-023-17372-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 11/29/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND #KindnessByPost (KbP) is a participatory public health initiative in which people anonymously send and receive cards containing messages of goodwill with others also taking part in the programme. Quantitative evaluations of KbP consistently find evidence of improvements to people's mental wellbeing and feelings of loneliness after participation and three months later. Our aim in the present study is to develop a programme theory of KbP, which describes for whom the KbP intervention improves mental wellbeing, other reported impacts, in which contexts it has these effects, and the mechanisms by which it works. METHODS We use a realist interviewing methodology to develop the programme theory. We conducted a focus group with the KbP executive team, and 20 one-to-one interviews with KbP participants. During analysis, a co-production working group iteratively developed a Theory of Change model comprising context-mechanism-outcome statements [CMOs] to map out the mechanisms present in KbP. RESULTS We developed 145 CMO statements, which we condensed and categorized into 32 overarching CMOs across nine thematic topics: access to scheme; pathways to involvement; resources; culture; giving post; receiving post; content of received post; community; long term impact. These CMOs set out pathways through which KbP benefited participants, including from doing something kind for someone else, of receiving post and appreciating the effort that went into it, and from the creative process of creating post and writing the messages inside them. Effects were sustained in part through people keeping the cards and through the social media communities that emerged around KbP. DISCUSSION Both giving and receiving post and the sense of community benefited participants and improved their mood and feelings of connectedness with others. Connection with a stranger, rather than friends or family, was also an important feature of the initiative for participants. Our wide range of CMO pathways by which KbP produced positive outcomes may mean that the intervention is applicable or adaptable across many communities and settings. Taken together with evidence from the quantitative evaluations, KbP is potentially an effective, low-cost, and highly scalable public health intervention for reducing loneliness and improving wellbeing.
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Affiliation(s)
| | - Katey Warran
- Social Biobehavioural Research Group, University College London, London, UK
- School of Health in Social Science, University of Edinburgh, Edinburgh, UK
| | - Kathleen Fraser
- Division of Psychiatry, University College London, London, UK
| | - Beverley Chipp
- Division of Psychiatry, University College London, London, UK
| | - Gail McGinnes
- Division of Psychiatry, University College London, London, UK
| | - Mike Towers
- Division of Psychiatry, University College London, London, UK
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21
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Zhou J, Sukhova K, Peacock TP, McKay PF, Brown JC, Frise R, Baillon L, Moshe M, Kugathasan R, Shattock RJ, Barclay WS. Omicron breakthrough infections in vaccinated or previously infected hamsters. Proc Natl Acad Sci U S A 2023; 120:e2308655120. [PMID: 37903249 PMCID: PMC10636328 DOI: 10.1073/pnas.2308655120] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/17/2023] [Indexed: 11/01/2023] Open
Abstract
The ongoing SARS-CoV-2 epidemic was marked by the repeated emergence and replacement of "variants" with genetic and phenotypic distance from the ancestral strains, the most recent examples being viruses of the Omicron lineage. Here, we describe a hamster direct contact exposure challenge model to assess protection against reinfection conferred by either vaccination or prior infection. We found that two doses of self-amplifying RNA vaccine based on the ancestral Spike ameliorated weight loss following Delta infection and decreased viral loads but had minimal effect on Omicron BA.1 infection. Prior vaccination followed by Delta or BA.1 breakthrough infections led to a high degree of cross-reactivity to all tested variants, suggesting that repeated exposure to antigenically distinct Spikes, via infection and/or vaccination drives a cross-reactive immune response. Prior infection with ancestral or Alpha variant was partially protective against BA.1 infection, whereas all animals previously infected with Delta and exposed to BA.1 became reinfected, although they shed less virus than BA.1-infected naive hamsters. Hamsters reinfected with BA.1 after prior Delta infection emitted infectious virus into the air, indicating that they could be responsible for onwards airborne transmission. We further tested whether prior infection with BA.1 protected from reinfection with Delta or later Omicron sublineages BA.2, BA.4, or BA.5. BA.1 was protective against BA.2 but not against Delta, BA.4, or BA.5 reinfection. These findings suggest that cohorts whose only immune experience of COVID-19 is Omicron BA.1 infection may be vulnerable to future circulation of reemerged Delta-like derivatives, as well as emerging Omicron sublineages.
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Affiliation(s)
- Jie Zhou
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Ksenia Sukhova
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Thomas P. Peacock
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Paul F. McKay
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Jonathan C. Brown
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Laury Baillon
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Maya Moshe
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Ruthiran Kugathasan
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Robin J. Shattock
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, LondonW2 1PG, United Kingdom
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22
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Neale I, Ali M, Kronsteiner B, Longet S, Abraham P, Deeks AS, Brown A, Moore SC, Stafford L, Dobson SL, Plowright M, Newman TAH, Wu MY, Carr EJ, Beale R, Otter AD, Hopkins S, Hall V, Tomic A, Payne RP, Barnes E, Richter A, Duncan CJA, Turtle L, de Silva TI, Carroll M, Lambe T, Klenerman P, Dunachie S. CD4+ and CD8+ T cells and antibodies are associated with protection against Delta vaccine breakthrough infection: a nested case-control study within the PITCH study. mBio 2023; 14:e0121223. [PMID: 37655880 PMCID: PMC10653804 DOI: 10.1128/mbio.01212-23] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/26/2023] [Indexed: 09/02/2023] Open
Abstract
IMPORTANCE Defining correlates of protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine breakthrough infection informs vaccine policy for booster doses and future vaccine designs. Existing studies demonstrate humoral correlates of protection, but the role of T cells in protection is still unclear. In this study, we explore antibody and T cell immune responses associated with protection against Delta variant vaccine breakthrough infection in a well-characterized cohort of UK Healthcare Workers (HCWs). We demonstrate evidence to support a role for CD4+ and CD8+ T cells as well as antibodies against Delta vaccine breakthrough infection. In addition, our results suggest a potential role for cross-reactive T cells in vaccine breakthrough.
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Affiliation(s)
- Isabel Neale
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Mohammad Ali
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephanie Longet
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Priyanka Abraham
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Alexandra S. Deeks
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Shona C. Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Lizzie Stafford
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Susan L. Dobson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Megan Plowright
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Thomas A. H. Newman
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Mary Y. Wu
- Covid Surveillance Unit, The Francis Crick Institute, London, United Kingdom
| | - Crick COVID Immunity Pipeline
- Covid Surveillance Unit, The Francis Crick Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | | | - Rupert Beale
- The Francis Crick Institute, London, United Kingdom
- UCL Department of Renal Medicine, Royal Free Hospital, London, United Kingdom
| | | | | | | | - Adriana Tomic
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
| | - Rebecca P. Payne
- Translational and Clinical Research Institute Immunity and Inflammation Theme, Newcastle University, Newcastle, United Kingdom
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Alex Richter
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Christopher J. A. Duncan
- Translational and Clinical Research Institute Immunity and Inflammation Theme, Newcastle University, Newcastle, United Kingdom
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | - Thushan I. de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Miles Carroll
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Teresa Lambe
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Susanna Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - On behalf of the PITCH Consortium
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
- Covid Surveillance Unit, The Francis Crick Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- UCL Department of Renal Medicine, Royal Free Hospital, London, United Kingdom
- UK Health Security Agency, Porton Down, United Kingdom
- UK Health Security Agency, London, United Kingdom
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
- Translational and Clinical Research Institute Immunity and Inflammation Theme, Newcastle University, Newcastle, United Kingdom
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
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23
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Seow J, Shalim ZA, Graham C, Kimuda S, Pillai A, Lechmere T, Kurshan A, Khimji AM, Snell LB, Nebbia G, Mant C, Waters A, Fox J, Malim MH, Doores KJ. Broad and potent neutralizing antibodies are elicited in vaccinated individuals following Delta/BA.1 breakthrough infection. mBio 2023; 14:e0120623. [PMID: 37747187 PMCID: PMC10653880 DOI: 10.1128/mbio.01206-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/02/2023] [Indexed: 09/26/2023] Open
Abstract
IMPORTANCE With the emergence of SARS-CoV-2 viral variants, there has been an increase in infections in vaccinated individuals. Here, we isolated monoclonal antibodies (mAbs) from individuals experiencing a breakthrough infection (Delta or BA.1) to determine how exposure to a heterologous Spike broadens the neutralizing antibody response at the monoclonal level. All mAbs isolated had reactivity to the Spike of the vaccine and infection variant. While many mAbs showed reduced neutralization of current circulating variants, we identified mAbs with broad and potent neutralization of BA.2.75.2, XBB, XBB.1.5, and BQ.1.1 indicating the presence of conserved epitopes on Spike. These results indicate that variant-based vaccine boosters have the potential to broaden the vaccine response.
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Affiliation(s)
- Jeffrey Seow
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Zayed A. Shalim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Simon Kimuda
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Aswin Pillai
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Thomas Lechmere
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ashwini Kurshan
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Atika M. Khimji
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Luke B. Snell
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Department of Infectious Diseases, Centre for Clinical Infection and Diagnostics Research, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Christine Mant
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Department of Infectious Diseases, Infectious Diseases Biobank, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Anele Waters
- Harrison Wing, Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Julie Fox
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
- Harrison Wing, Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Katie J. Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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24
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Sannino DR, Dobson AJ. Acetobacter pomorum in the Drosophila gut microbiota buffers against host metabolic impacts of dietary preservative formula and batch variation in dietary yeast. Appl Environ Microbiol 2023; 89:e0016523. [PMID: 37800920 PMCID: PMC10617557 DOI: 10.1128/aem.00165-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 08/05/2023] [Indexed: 10/07/2023] Open
Abstract
Gut microbiota are fundamentally important for healthy function in animal hosts. Drosophila melanogaster is a powerful system for understanding host-microbiota interactions, with modulation of the microbiota inducing phenotypic changes that are conserved across animal taxa. Qualitative differences in diet, such as preservatives and dietary yeast batch variation, may affect fly health indirectly via microbiota, and may potentially have hitherto uncharacterized effects directly on the fly. These factors are rarely considered, controlled, and are not standardized among laboratories. Here, we show that the microbiota's impact on fly triacylglyceride (TAG) levels-a commonly-measured metabolic index-depends on both preservatives and yeast, and combinatorial interactions among the three variables. In studies of conventional, axenic, and gnotobiotic flies, we found that microbial impacts were apparent only on specific yeast-by-preservative conditions, with TAG levels determined by a tripartite interaction of the three experimental factors. When comparing axenic and conventional flies, we found that preservatives caused more variance in host TAG than microbiota status, and certain yeast-preservative combinations even reversed effects of microbiota on TAG. Preservatives had major effects in axenic flies, suggesting either direct effects on the fly or indirect effects via media. However, Acetobacter pomorum buffers the fly against this effect, despite the preservatives inhibiting growth, indicating that this bacterium benefits the host in the face of mutual environmental toxicity. Our results suggest that antimicrobial preservatives have major impacts on host TAG, and that microbiota modulates host TAG dependent on the combination of the dietary factors of preservative formula and yeast batch. IMPORTANCE Drosophila melanogaster is a premier model for microbiome science, which has greatly enhanced our understanding of the basic biology of host-microbe interactions. However, often overlooked factors such as dietary composition, including yeast batch variability and preservative formula, may confound data interpretation of experiments within the same lab and lead to different findings when comparing between labs. Our study supports this notion; we find that the microbiota does not alter host TAG levels independently. Rather, TAG is modulated by combinatorial effects of microbiota, yeast batch, and preservative formula. Specific preservatives increase TAG even in germ-free flies, showing that a commonplace procedure in fly husbandry alters metabolic physiology. This work serves as a cautionary tale that fly rearing methodology can mask or drive microbiota-dependent metabolic changes and also cause microbiota-independent changes.
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Affiliation(s)
- David R. Sannino
- School of Molecular Biosciences, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Adam J. Dobson
- School of Molecular Biosciences, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
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25
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Abrudan MI, Shamanna V, Prasanna A, Underwood A, Argimón S, Nagaraj G, Di Gregorio S, Govindan V, Vasanth A, Dharmavaram S, Kekre M, Aanensen DM, Ravikumar KL. Novel multidrug-resistant sublineages of Staphylococcus aureus clonal complex 22 discovered in India. mSphere 2023; 8:e0018523. [PMID: 37698417 PMCID: PMC10597471 DOI: 10.1128/msphere.00185-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/13/2023] [Indexed: 09/13/2023] Open
Abstract
Staphylococcus aureus is a major pathogen in India causing community and nosocomial infections, but little is known about its molecular epidemiology and mechanisms of resistance in hospital settings. Here, we use whole-genome sequencing (WGS) to characterize 478 S. aureus clinical isolates (393 methicillin-resistant Staphylococcus aureus (MRSA) and 85 methicilin-sensitive Staphylococcus aureus (MSSA) collected from 17 sentinel sites across India between 2014 and 2019. Sequencing results confirmed that sequence type 22 (ST22) (142 isolates, 29.7%), ST239 (74 isolates, 15.48%), and ST772 (67 isolates, 14%) were the most common clones. An in-depth analysis of 175 clonal complex (CC) 22 Indian isolates identified two novel ST22 MRSA lineages, both Panton-Valentine leukocidin+, both resistant to fluoroquinolones and aminoglycosides, and one harboring the the gene for toxic shock syndrome toxin 1 (tst). A temporal analysis of 1797 CC22 global isolates from 14 different studies showed that the two Indian ST22 lineages shared a common ancestor in 1984 (95% highest posterior density [HPD]: 1982-1986), as well as evidence of transmission to other parts of the world. Moreover, the study also gives a comprehensive view of ST2371, a sublineage of CC22, as a new emerging lineage in India and describes it in relationship with the other Indian ST22 isolates. In addition, the retrospective identification of a putative outbreak of multidrug-resistant (MDR) ST239 from a single hospital in Bangalore that persisted over a period of 3 years highlights the need for the implementation of routine surveillance and simple infection prevention and control measures to reduce these outbreaks. To our knowledge, this is the first WGS study that characterized CC22 in India and showed that the Indian clones are distinct from the EMRSA-15 clone. Thus, with the improved resolution afforded by WGS, this study substantially contributed to our understanding of the global population of MRSA. IMPORTANCE The study conducted in India between 2014 and 2019 presents novel insights into the prevalence of MRSA in the region. Previous studies have characterized two dominant clones of MRSA in India, ST772 and ST239, using whole-genome sequencing. However, this study is the first to describe the third dominant clone, ST22, using the same approach. The ST22 Indian isolates were analyzed in-depth, leading to the discovery of two new sublineages of hospital-acquired Staphylococcus aureus in India, both carrying antimicrobial resistance genes and mutations, which limit treatment options for patients. One of the newly characterized sublineages, second Indian cluster, carries the tsst-1 virulence gene, increasing the risk of severe infections. The geographic spread of the two novel lineages, both within India and internationally, could pose a global public health threat. The study also sheds light on ST2371 in India, a single-locus variant of ST22. The identification of a putative outbreak of MDR ST239 in a single hospital in Bangalore emphasizes the need for routine surveillance and simple infection prevention and control measures to reduce these outbreaks. Overall, this study significantly contributes to our understanding of the global population of MRSA, thanks to the improved resolution afforded by WGS.
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Affiliation(s)
- Monica I. Abrudan
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Genome Campus, Hinxton, United Kingdom
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
- Department of Biotechnology, NMAM Institute of Technology, Nitte (Deemed to be University), Mangalore, India
| | - Akshatha Prasanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Sabrina Di Gregorio
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Vandana Govindan
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Ashwini Vasanth
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Sravani Dharmavaram
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Mihir Kekre
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - K. L. Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
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26
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Williams CJ, Elliott F, Sapanara N, Aghaei F, Zhang L, Muranyi A, Yan D, Bai I, Zhao Z, Shires M, Wood HM, Richman SD, Hemmings G, Hale M, Bottomley D, Galvin L, Cartlidge C, Dance S, Bacon CM, Mansfield L, Young-Zvandasara K, Sudan A, Lambert K, Bibby I, Coupland SE, Montazeri A, Kipling N, Hughes K, Cross SS, Dewdney A, Pheasey L, Leng C, Gochera T, Mangham DC, Saunders M, Pritchard M, Stott H, Mukherjee A, Ilyas M, Silverman R, Hyland G, Sculthorpe D, Thornton K, Gould I, O'Callaghan A, Brown N, Turnbull S, Shaw L, Seymour MT, West NP, Seligmann JF, Singh S, Shanmugam K, Quirke P. Associations between AI-Assisted Tumor Amphiregulin and Epiregulin IHC and Outcomes from Anti-EGFR Therapy in the Routine Management of Metastatic Colorectal Cancer. Clin Cancer Res 2023; 29:4153-4165. [PMID: 37363997 PMCID: PMC10570673 DOI: 10.1158/1078-0432.ccr-23-0859] [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: 03/24/2023] [Revised: 05/31/2023] [Accepted: 06/22/2023] [Indexed: 06/28/2023]
Abstract
PURPOSE High tumor production of the EGFR ligands, amphiregulin (AREG) and epiregulin (EREG), predicted benefit from anti-EGFR therapy for metastatic colorectal cancer (mCRC) in a retrospective analysis of clinical trial data. Here, AREG/EREG IHC was analyzed in a cohort of patients who received anti-EGFR therapy as part of routine care, including key clinical contexts not investigated in the previous analysis. EXPERIMENTAL DESIGN Patients who received panitumumab or cetuximab ± chemotherapy for treatment of RAS wild-type mCRC at eight UK cancer centers were eligible. Archival formalin-fixed paraffin-embedded tumor tissue was analyzed for AREG and EREG IHC in six regional laboratories using previously developed artificial intelligence technologies. Primary endpoints were progression-free survival (PFS) and overall survival (OS). RESULTS A total of 494 of 541 patients (91.3%) had adequate tissue for analysis. A total of 45 were excluded after central extended RAS testing, leaving 449 patients in the primary analysis population. After adjustment for additional prognostic factors, high AREG/EREG expression (n = 360; 80.2%) was associated with significantly prolonged PFS [median: 8.5 vs. 4.4 months; HR, 0.73; 95% confidence interval (CI), 0.56-0.95; P = 0.02] and OS [median: 16.4 vs. 8.9 months; HR, 0.66 95% CI, 0.50-0.86; P = 0.002]. The significant OS benefit was maintained among patients with right primary tumor location (PTL), those receiving cetuximab or panitumumab, those with an oxaliplatin- or irinotecan-based chemotherapy backbone, and those with tumor tissue obtained by biopsy or surgical resection. CONCLUSIONS High tumor AREG/EREG expression was associated with superior survival outcomes from anti-EGFR therapy in mCRC, including in right PTL disease. AREG/EREG IHC assessment could aid therapeutic decisions in routine practice. See related commentary by Randon and Pietrantonio, p. 4021.
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Affiliation(s)
- Christopher J.M. Williams
- Division of Pathology and Data Analytics, University of Leeds, Leeds, United Kingdom
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Faye Elliott
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Nancy Sapanara
- Medical & Scientific Affairs, Roche Molecular Systems Inc., Tucson, Arizona
| | - Faranak Aghaei
- Medical & Scientific Affairs, Roche Molecular Systems Inc., Tucson, Arizona
| | - Liping Zhang
- Medical & Scientific Affairs, Roche Molecular Systems Inc., Tucson, Arizona
| | - Andrea Muranyi
- Medical & Scientific Affairs, Roche Molecular Systems Inc., Tucson, Arizona
| | - Dongyao Yan
- Medical & Scientific Affairs, Roche Molecular Systems Inc., Tucson, Arizona
| | - Isaac Bai
- Medical & Scientific Affairs, Roche Molecular Systems Inc., Tucson, Arizona
| | - Zuo Zhao
- Imaging and Algorithms, Digital Pathology, Roche Sequencing Solutions Inc., Santa Clara, California
| | - Michael Shires
- Division of Pathology and Data Analytics, University of Leeds, Leeds, United Kingdom
| | - Henry M. Wood
- Division of Pathology and Data Analytics, University of Leeds, Leeds, United Kingdom
| | - Susan D. Richman
- Division of Pathology and Data Analytics, University of Leeds, Leeds, United Kingdom
| | - Gemma Hemmings
- Division of Pathology and Data Analytics, University of Leeds, Leeds, United Kingdom
| | - Michael Hale
- Division of Pathology and Data Analytics, University of Leeds, Leeds, United Kingdom
| | - Daniel Bottomley
- Division of Pathology and Data Analytics, University of Leeds, Leeds, United Kingdom
| | - Leanne Galvin
- Division of Pathology and Data Analytics, University of Leeds, Leeds, United Kingdom
| | - Caroline Cartlidge
- Division of Pathology and Data Analytics, University of Leeds, Leeds, United Kingdom
| | - Sarah Dance
- Medical Affairs, Access and Innovation, Roche Diagnostics Limited, Burgess Hill, United Kingdom
| | - Chris M. Bacon
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Laura Mansfield
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | - Ajay Sudan
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Katy Lambert
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Irena Bibby
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Sarah E. Coupland
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Amir Montazeri
- The Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - Natalie Kipling
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Kathryn Hughes
- The Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - Simon S. Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Alice Dewdney
- Weston Park Cancer Centre, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | - Leanne Pheasey
- Weston Park Cancer Centre, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | - Cathryn Leng
- Weston Park Cancer Centre, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | - Tatenda Gochera
- Weston Park Cancer Centre, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | - D. Chas Mangham
- Adult Histopathology, Laboratory Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom
| | - Mark Saunders
- The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Martin Pritchard
- Adult Histopathology, Laboratory Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom
| | - Helen Stott
- The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Abhik Mukherjee
- Translational Medical Sciences, Cancer and Stem Cells, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Mohammad Ilyas
- Translational Medical Sciences, Cancer and Stem Cells, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Rafael Silverman
- Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Georgina Hyland
- Translational Medical Sciences, Cancer and Stem Cells, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Declan Sculthorpe
- Translational Medical Sciences, Cancer and Stem Cells, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Kirsty Thornton
- Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Imogen Gould
- Translational Medical Sciences, Cancer and Stem Cells, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | | | - Nicholas Brown
- Calderdale and Huddersfield NHS Foundation Trust, Huddersfield, United Kingdom
| | - Samantha Turnbull
- Calderdale and Huddersfield NHS Foundation Trust, Huddersfield, United Kingdom
| | - Lisa Shaw
- Calderdale and Huddersfield NHS Foundation Trust, Huddersfield, United Kingdom
| | - Matthew T. Seymour
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Nicholas P. West
- Division of Pathology and Data Analytics, University of Leeds, Leeds, United Kingdom
| | - Jenny F. Seligmann
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Shalini Singh
- Medical & Scientific Affairs, Roche Molecular Systems Inc., Tucson, Arizona
| | - Kandavel Shanmugam
- Medical & Scientific Affairs, Roche Molecular Systems Inc., Tucson, Arizona
| | - Philip Quirke
- Division of Pathology and Data Analytics, University of Leeds, Leeds, United Kingdom
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Shukla VK, Siemons L, Hansen DF. Intrinsic structural dynamics dictate enzymatic activity and inhibition. Proc Natl Acad Sci U S A 2023; 120:e2310910120. [PMID: 37782780 PMCID: PMC10576142 DOI: 10.1073/pnas.2310910120] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/14/2023] [Indexed: 10/04/2023] Open
Abstract
Enzymes are known to sample various conformations, many of which are critical for their biological function. However, structural characterizations of enzymes predominantly focus on the most populated conformation. As a result, single-point mutations often produce structures that are similar or essentially identical to those of the wild-type enzyme despite large changes in enzymatic activity. Here, we show for mutants of a histone deacetylase enzyme (HDAC8) that reduced enzymatic activities, reduced inhibitor affinities, and reduced residence times are all captured by the rate constants between intrinsically sampled conformations that, in turn, can be obtained independently by solution NMR spectroscopy. Thus, for the HDAC8 enzyme, the dynamic sampling of conformations dictates both enzymatic activity and inhibitor potency. Our analysis also dissects the functional role of the conformations sampled, where specific conformations distinct from those in available structures are responsible for substrate and inhibitor binding, catalysis, and product dissociation. Precise structures alone often do not adequately explain the effect of missense mutations on enzymatic activity and drug potency. Our findings not only assign functional roles to several conformational states of HDAC8 but they also underscore the paramount role of dynamics, which will have general implications for characterizing missense mutations and designing inhibitors.
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Affiliation(s)
- Vaibhav Kumar Shukla
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Lucas Siemons
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - D. Flemming Hansen
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, LondonWC1E 6BT, United Kingdom
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28
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Lim CM, González Díaz A, Fuxreiter M, Pun FW, Zhavoronkov A, Vendruscolo M. Multiomic prediction of therapeutic targets for human diseases associated with protein phase separation. Proc Natl Acad Sci U S A 2023; 120:e2300215120. [PMID: 37774095 PMCID: PMC10556643 DOI: 10.1073/pnas.2300215120] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 08/02/2023] [Indexed: 10/01/2023] Open
Abstract
The phenomenon of protein phase separation (PPS) underlies a wide range of cellular functions. Correspondingly, the dysregulation of the PPS process has been associated with numerous human diseases. To enable therapeutic interventions based on the regulation of this association, possible targets should be identified. For this purpose, we present an approach that combines the multiomic PandaOmics platform with the FuzDrop method to identify PPS-prone disease-associated proteins. Using this approach, we prioritize candidates with high PandaOmics and FuzDrop scores using a profiling method that accounts for a wide range of parameters relevant for disease mechanism and pharmacological intervention. We validate the differential phase separation behaviors of three predicted Alzheimer's disease targets (MARCKS, CAMKK2, and p62) in two cell models of this disease. Overall, the approach that we present generates a list of possible therapeutic targets for human diseases associated with the dysregulation of the PPS process.
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Affiliation(s)
- Christine M. Lim
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Alicia González Díaz
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Padova35131, Italy
| | - Frank W. Pun
- Insilico Medicine, Hong Kong Science and Technology Park, Hong Kong, China
| | - Alex Zhavoronkov
- Insilico Medicine, Hong Kong Science and Technology Park, Hong Kong, China
| | - Michele Vendruscolo
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
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29
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Ramans-Harborough S, Kalverda AP, Manfield IW, Thompson GS, Kieffer M, Uzunova V, Quareshy M, Prusinska JM, Roychoudhry S, Hayashi KI, Napier R, del Genio C, Kepinski S. Intrinsic disorder and conformational coexistence in auxin coreceptors. Proc Natl Acad Sci U S A 2023; 120:e2221286120. [PMID: 37756337 PMCID: PMC10556615 DOI: 10.1073/pnas.2221286120] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/17/2023] [Indexed: 09/29/2023] Open
Abstract
AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) transcriptional repressor proteins and the TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB) proteins to which they bind act as auxin coreceptors. While the structure of TIR1 has been solved, structural characterization of the regions of the Aux/IAA protein responsible for auxin perception has been complicated by their predicted disorder. Here, we use NMR, CD and molecular dynamics simulation to investigate the N-terminal domains of the Aux/IAA protein IAA17/AXR3. We show that despite the conformational flexibility of the region, a critical W-P bond in the core of the Aux/IAA degron motif occurs at a strikingly high (1:1) ratio of cis to trans isomers, consistent with the requirement of the cis conformer for the formation of the fully-docked receptor complex. We show that the N-terminal half of AXR3 is a mixture of multiple transiently structured conformations with a propensity for two predominant and distinct conformational subpopulations within the overall ensemble. These two states were modeled together with the C-terminal PB1 domain to provide the first complete simulation of an Aux/IAA. Using MD to recreate the assembly of each complex in the presence of auxin, both structural arrangements were shown to engage with the TIR1 receptor, and contact maps from the simulations match closely observations of NMR signal-decreases. Together, our results and approach provide a platform for exploring the functional significance of variation in the Aux/IAA coreceptor family and for understanding the role of intrinsic disorder in auxin signal transduction and other signaling systems.
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Affiliation(s)
- Sigurd Ramans-Harborough
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Arnout P. Kalverda
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Iain W. Manfield
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Gary S. Thompson
- Wellcome Biological Nuclear Magnetic Resonance Facility, Division of Natural Sciences, University of Kent, CanterburyCT2 7NJ, United Kingdom
| | - Martin Kieffer
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Veselina Uzunova
- School of Life Sciences, University of Warwick, CoventryCV4 7AL, United Kingdom
| | - Mussa Quareshy
- School of Life Sciences, University of Warwick, CoventryCV4 7AL, United Kingdom
| | | | - Suruchi Roychoudhry
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Ken-ichiro Hayashi
- Department of Bioscience, Okayama University of Science, Okayama700-0005, Japan
| | - Richard Napier
- School of Life Sciences, University of Warwick, CoventryCV4 7AL, United Kingdom
| | - Charo del Genio
- Centre for Fluid and Complex Systems, Coventry University, CoventryCV1 5FB, United Kingdom
| | - Stefan Kepinski
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
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30
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Hutton W, Allman E, McKeown C, Singer AC, Roberts AP. Complete genome sequence of mcr-9 containing Leclercia adecarboxylata. Microbiol Resour Announc 2023; 12:e0048123. [PMID: 37578246 PMCID: PMC10508152 DOI: 10.1128/mra.00481-23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023] Open
Abstract
Here, we provide the genome sequence of a Leclercia adecarboxylata isolated from a screen of an environmental bacterial isolate library for resistance to the plant flavonoid berberine. We detected the colistin resistance gene mcr-9, located on an IncFII(pECLA) plasmid.
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Affiliation(s)
- William Hutton
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Ellie Allman
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Claudia McKeown
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Andrew C. Singer
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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31
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Allen ME, Hindley JW, O’Toole N, Cooke HS, Contini C, Law RV, Ces O, Elani Y. Biomimetic behaviors in hydrogel artificial cells through embedded organelles. Proc Natl Acad Sci U S A 2023; 120:e2307772120. [PMID: 37603747 PMCID: PMC10466294 DOI: 10.1073/pnas.2307772120] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/13/2023] [Indexed: 08/23/2023] Open
Abstract
Artificial cells are biomimetic structures formed from molecular building blocks that replicate biological processes, behaviors, and architectures. Of these building blocks, hydrogels have emerged as ideal, yet underutilized candidates to provide a gel-like chassis in which to incorporate both biological and nonbiological componentry which enables the replication of cellular functionality. Here, we demonstrate a microfluidic strategy to assemble biocompatible cell-sized hydrogel-based artificial cells with a variety of different embedded functional subcompartments, which act as engineered synthetic organelles. The organelles enable the recreation of increasingly biomimetic behaviors, including stimulus-induced motility, content release through activation of membrane-associated proteins, and enzymatic communication with surrounding bioinspired compartments. In this way, we showcase a foundational strategy for the bottom-up construction of hydrogel-based artificial cell microsystems which replicate fundamental cellular behaviors, paving the way for the construction of next-generation biotechnological devices.
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Affiliation(s)
- Matthew E. Allen
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - James W. Hindley
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Nina O’Toole
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Hannah S. Cooke
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Claudia Contini
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Robert V. Law
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Oscar Ces
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, LondonSW7 2AZ, UK
- FabriCELL, Imperial College London, Molecular Sciences Research Hub, LondonW12 0BZ, UK
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32
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Checchi F, Jarvis CI, van Zandvoort K, Warsame A. Mortality among populations affected by armed conflict in northeast Nigeria, 2016 to 2019. Proc Natl Acad Sci U S A 2023; 120:e2217601120. [PMID: 37467271 PMCID: PMC10372555 DOI: 10.1073/pnas.2217601120] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 06/12/2023] [Indexed: 07/21/2023] Open
Abstract
Armed conflict, displacement and food insecurity have affected Adamawa, Borno, and Yobe states of northeast Nigeria (population ≈ 12 million) since 2009. Insecurity escalated in 2013 to 2015, but the humanitarian response was delayed and the crisis' health impact was unquantified due to incomplete death registration and limited ground access. We estimated mortality attributable to this crisis using a small-area estimation approach that circumvented these challenges. We fitted a mixed effects model to household mortality data collected as part of 70 ground surveys implemented by humanitarian actors. Model predictors, drawn from existing data, included livelihood typology, staple cereal price, vaccination geocoverage, and humanitarian actor presence. To project accurate death tolls, we reconstructed population denominators based on forced displacement. We used the model and population estimates to project mortality under observed conditions and varying assumed counterfactual conditions, had there been no crisis, with the difference providing excess mortality. Death rates were highly elevated across most ground surveys, with net negative household migration. Between April 2016 and December 2019, we projected 490,000 excess deaths (230,000 children under 5 y) in the most likely counterfactual scenario, with a range from 90,000 (best-case) to 550,000 (worst-case). Death rates were two to three times higher than counterfactual levels, double the projected national rate, and highest in 2016 to 2017. Despite limited scope (we could not study the situation before 2016 or in neighboring affected countries), our findings suggest a staggering health impact of this crisis. Further studies to document mortality in this and other crises are needed to guide decision-making and memorialize their human toll.
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Affiliation(s)
- Francesco Checchi
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Christopher I Jarvis
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Kevin van Zandvoort
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Abdihamid Warsame
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
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Thompson CR, Torres PM, Kontogianni K, Byrne RL, Noguera SV, Luna-Muschi A, Marchi AP, Andrade PS, dos Santos Barboza A, Nishikawara M, Body R, de Vos M, Escadafal C, Adams E, Figueiredo Costa S, Cubas-Atienzar AI. Multicenter Diagnostic Evaluation of OnSite COVID-19 Rapid Test (CTK Biotech) among Symptomatic Individuals in Brazil and the United Kingdom. Microbiol Spectr 2023; 11:e0504422. [PMID: 37212699 PMCID: PMC10269675 DOI: 10.1128/spectrum.05044-22] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/17/2023] [Indexed: 05/23/2023] Open
Abstract
The COVID-19 pandemic has given rise to numerous commercially available antigen rapid diagnostic tests (Ag-RDTs). To generate and to share accurate and independent data with the global community requires multisite prospective diagnostic evaluations of Ag-RDTs. This report describes the clinical evaluation of the OnSite COVID-19 rapid test (CTK Biotech, CA, USA) in Brazil and the United Kingdom. A total of 496 paired nasopharyngeal (NP) swabs were collected from symptomatic health care workers at Hospital das Clínicas in São Paulo, Brazil, and 211 NP swabs were collected from symptomatic participants at a COVID-19 drive-through testing site in Liverpool, United Kingdom. Swabs were analyzed by Ag-RDT, and results were compared to quantitative reverse transcriptase PCR (RT-qPCR). The clinical sensitivity of the OnSite COVID-19 rapid test in Brazil was 90.3% (95% confidence interval [CI], 75.1 to 96.7%) and in the United Kingdom was 75.3% (95% CI, 64.6 to 83.6%). The clinical specificity in Brazil was 99.4% (95% CI, 98.1 to 99.8%) and in the United Kingdom was 95.5% (95% CI, 90.6 to 97.9%). Concurrently, analytical evaluation of the Ag-RDT was assessed using direct culture supernatant of SARS-CoV-2 strains from wild-type (WT), Alpha, Delta, Gamma, and Omicron lineages. This study provides comparative performance of an Ag-RDT across two different settings, geographical areas, and populations. Overall, the OnSite Ag-RDT demonstrated a lower clinical sensitivity than claimed by the manufacturer. The sensitivity and specificity from the Brazil study fulfilled the performance criteria determined by the World Health Organization, but the performance obtained from the UK study failed to do. Further evaluation of Ag-RDTs should include harmonized protocols between laboratories to facilitate comparison between settings. IMPORTANCE Evaluating rapid diagnostic tests in diverse populations is essential to improving diagnostic responses as it gives an indication of the accuracy in real-world scenarios. In the case of rapid diagnostic testing within this pandemic, lateral flow tests that meet the minimum requirements for sensitivity and specificity can play a key role in increasing testing capacity, allowing timely clinical management of those infected, and protecting health care systems. This is particularly valuable in settings where access to the test gold standard is often restricted.
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Affiliation(s)
- Caitlin R. Thompson
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
| | - Pablo Muñoz Torres
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Konstantina Kontogianni
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
| | - Rachel L. Byrne
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
| | - LSTM Diagnostic group
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Epidemiology, School of Public Health of University of São Paulo, São Paulo, Brazil
- Centro de atendimento ao colaborador, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Divisão de Laboratório Central, Hospital das Clinicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- FIND, Geneva, Switzerland
- Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Global Access Diagnostics, Thurleigh, Bedfordshire, United Kingdom
| | - Saidy Vásconez Noguera
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Alessandra Luna-Muschi
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ana Paula Marchi
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pâmela S. Andrade
- Department of Epidemiology, School of Public Health of University of São Paulo, São Paulo, Brazil
| | - Antonio dos Santos Barboza
- Centro de atendimento ao colaborador, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Marli Nishikawara
- Centro de atendimento ao colaborador, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - CONDOR steering group
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Epidemiology, School of Public Health of University of São Paulo, São Paulo, Brazil
- Centro de atendimento ao colaborador, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Divisão de Laboratório Central, Hospital das Clinicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- FIND, Geneva, Switzerland
- Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Global Access Diagnostics, Thurleigh, Bedfordshire, United Kingdom
| | - Richard Body
- Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Camille Escadafal
- Divisão de Laboratório Central, Hospital das Clinicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Emily Adams
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
- Global Access Diagnostics, Thurleigh, Bedfordshire, United Kingdom
| | - Silvia Figueiredo Costa
- LIM-49, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ana I. Cubas-Atienzar
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
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Cutforth M, Watson H, Brown C, Wang C, Thomson S, Fell D, Dilys V, Scrimgeour M, Schrempf P, Lesh J, Muir K, Weir A, O’Neil AQ. Acute stroke CDS: automatic retrieval of thrombolysis contraindications from unstructured clinical letters. Front Digit Health 2023; 5:1186516. [PMID: 37388253 PMCID: PMC10305776 DOI: 10.3389/fdgth.2023.1186516] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/15/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction Thrombolysis treatment for acute ischaemic stroke can lead to better outcomes if administered early enough. However, contraindications exist which put the patient at greater risk of a bleed (e.g. recent major surgery, anticoagulant medication). Therefore, clinicians must check a patient's past medical history before proceeding with treatment. In this work we present a machine learning approach for accurate automatic detection of this information in unstructured text documents such as discharge letters or referral letters, to support the clinician in making a decision about whether to administer thrombolysis. Methods We consulted local and national guidelines for thrombolysis eligibility, identifying 86 entities which are relevant to the thrombolysis decision. A total of 8,067 documents from 2,912 patients were manually annotated with these entities by medical students and clinicians. Using this data, we trained and validated several transformer-based named entity recognition (NER) models, focusing on transformer models which have been pre-trained on a biomedical corpus as these have shown most promise in the biomedical NER literature. Results Our best model was a PubMedBERT-based approach, which obtained a lenient micro/macro F1 score of 0.829/0.723. Ensembling 5 variants of this model gave a significant boost to precision, obtaining micro/macro F1 of 0.846/0.734 which approaches the human annotator performance of 0.847/0.839. We further propose numeric definitions for the concepts of name regularity (similarity of all spans which refer to an entity) and context regularity (similarity of all context surrounding mentions of an entity), using these to analyse the types of errors made by the system and finding that the name regularity of an entity is a stronger predictor of model performance than raw training set frequency. Discussion Overall, this work shows the potential of machine learning to provide clinical decision support (CDS) for the time-critical decision of thrombolysis administration in ischaemic stroke by quickly surfacing relevant information, leading to prompt treatment and hence to better patient outcomes.
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Affiliation(s)
| | - Hannah Watson
- Canon Medical Research Europe, Edinburgh, United Kingdom
| | - Cameron Brown
- Institute of Neuroscience & Psychology, University of Glasgow, Glasgow, United Kingdom
| | - Chaoyang Wang
- Canon Medical Research Europe, Edinburgh, United Kingdom
| | - Stuart Thomson
- Canon Medical Research Europe, Edinburgh, United Kingdom
| | - Dickon Fell
- Canon Medical Research Europe, Edinburgh, United Kingdom
| | | | | | | | - James Lesh
- Canon Medical Research Europe, Edinburgh, United Kingdom
| | - Keith Muir
- Institute of Neuroscience & Psychology, University of Glasgow, Glasgow, United Kingdom
| | - Alexander Weir
- Canon Medical Research Europe, Edinburgh, United Kingdom
| | - Alison Q O’Neil
- Canon Medical Research Europe, Edinburgh, United Kingdom
- School of Engineering, University of Edinburgh, Edinburgh, United Kingdom
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35
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Bedran G, Gasser HC, Weke K, Wang T, Bedran D, Laird A, Battail C, Zanzotto FM, Pesquita C, Axelson H, Rajan A, Harrison DJ, Palkowski A, Pawlik M, Parys M, O'Neill JR, Brennan PM, Symeonides SN, Goodlett DR, Litchfield K, Fahraeus R, Hupp TR, Kote S, Alfaro JA. The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I-Associated Peptides. Cancer Immunol Res 2023; 11:747-762. [PMID: 36961404 PMCID: PMC10236148 DOI: 10.1158/2326-6066.cir-22-0621] [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: 08/01/2022] [Revised: 11/25/2022] [Accepted: 03/16/2023] [Indexed: 03/25/2023]
Abstract
Tumor antigens can emerge through multiple mechanisms, including translation of noncoding genomic regions. This noncanonical category of tumor antigens has recently gained attention; however, our understanding of how they recur within and between cancer types is still in its infancy. Therefore, we developed a proteogenomic pipeline based on deep learning de novo mass spectrometry (MS) to enable the discovery of noncanonical MHC class I-associated peptides (ncMAP) from noncoding regions. Considering that the emergence of tumor antigens can also involve posttranslational modifications (PTM), we included an open search component in our pipeline. Leveraging the wealth of MS-based immunopeptidomics, we analyzed data from 26 MHC class I immunopeptidomic studies across 11 different cancer types. We validated the de novo identified ncMAPs, along with the most abundant PTMs, using spectral matching and controlled their FDR to 1%. The noncanonical presentation appeared to be 5 times enriched for the A03 HLA supertype, with a projected population coverage of 55%. The data reveal an atlas of 8,601 ncMAPs with varying levels of cancer selectivity and suggest 17 cancer-selective ncMAPs as attractive therapeutic targets according to a stringent cutoff. In summary, the combination of the open-source pipeline and the atlas of ncMAPs reported herein could facilitate the identification and screening of ncMAPs as targets for T-cell therapies or vaccine development.
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Affiliation(s)
- Georges Bedran
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Kenneth Weke
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Tongjie Wang
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Dominika Bedran
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Alexander Laird
- Urology Department, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Christophe Battail
- CEA, Grenoble Alpes University, INSERM, IRIG, Biosciences and Bioengineering for Health Laboratory (BGE) - UA13 INSERM-CEA-UGA, Grenoble, France
| | | | - Catia Pesquita
- LASIGE, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Håkan Axelson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ajitha Rajan
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - David J. Harrison
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Aleksander Palkowski
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Maciej Pawlik
- Academic Computer Centre CYFRONET, AGH University of Science and Technology, Cracow, Poland
| | - Maciej Parys
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - J. Robert O'Neill
- Cambridge Oesophagogastric Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Paul M. Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Stefan N. Symeonides
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - David R. Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
- University of Victoria Genome BC Proteome Centre, Victoria, Canada
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Paris, France
| | - Ted R. Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Javier A. Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
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Henehan MJ, Witts JD. Continental flood basalts do not drive later Phanerozoic extinctions. Proc Natl Acad Sci U S A 2023; 120:e2303700120. [PMID: 37186834 DOI: 10.1073/pnas.2303700120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Affiliation(s)
- Michael J Henehan
- Bristol Palaeobiology Research Group, School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, United Kingdom
| | - James D Witts
- Bristol Palaeobiology Research Group, School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, United Kingdom
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Landsberger M, Quick J, Mercer J. Coding-Complete Genome Sequences of Copenhagen and Copenhagen-Derived vP811 Strains of Vaccinia Virus Isolated from Cell Culture. Microbiol Resour Announc 2023; 12:e0009023. [PMID: 36946721 PMCID: PMC10112197 DOI: 10.1128/mra.00090-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/13/2023] [Indexed: 03/23/2023] Open
Abstract
The coding-complete genomes of laboratory vaccinia virus strain Copenhagen and the Copenhagen-derived deletion strain, vP811, were determined by short-read sequencing. Relative to the NCBI reference genome M35027, seven common coding differences were revealed, including an intact copy of the vaccinia virus immunomodulator A46R in both Cop and vP811.
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Affiliation(s)
- Mariann Landsberger
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Joshua Quick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Jason Mercer
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
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Suen KM, Sheard TM, Lin CC, Milonaityte D, Jayasinghe I, Ladbury JE. Expansion microscopy reveals subdomains in C. elegans germ granules. Life Sci Alliance 2023; 6:e202201650. [PMID: 36750365 PMCID: PMC9905708 DOI: 10.26508/lsa.202201650] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
Light and electron microscopy techniques have been indispensable in the identification and characterization of liquid-liquid phase separation membraneless organelles. However, for complex membraneless organelles such as the perinuclear germ granule in C. elegans, our understanding of how the intact organelle is regulated is hampered by (1) technical limitations in confocal fluorescence imaging for the simultaneous examination of multiple granule protein markers and (2) inaccessibility of electron microscopy. We take advantage of the newly developed super resolution method of expansion microscopy (ExM) and in situ staining of the whole proteome to examine the C. elegans germ granule, the P granule. We show that in small RNA pathway mutants, the P granule is smaller compared with WT animals. Furthermore, we investigate the relationship between the P granule and two other germ granules, Mutator foci and Z granule, and show that they are located within the same protein-dense regions while occupying distinct subdomains within this ultrastructure. This study will serve as an important tool in our understanding of germ granule biology and the biological role of liquid-liquid phase separation.
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Affiliation(s)
- Kin M Suen
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | | | - Chi-Chuan Lin
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Dovile Milonaityte
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Izzy Jayasinghe
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - John E Ladbury
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
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Sharratt K, Mason SJ, Kirkman G, Willmott D, McDermott D, Timmins S, Wager NM. Childhood Abuse and Neglect, Exposure to Domestic Violence and Sibling Violence: Profiles and Associations With Sociodemographic Variables and Mental Health Indicators. J Interpers Violence 2023; 38:NP1141-NP1162. [PMID: 35445607 PMCID: PMC9709533 DOI: 10.1177/08862605221090562] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Research indicates substantial overlap between child abuse and neglect (CAN), exposure to domestic violence and sibling abuse, with multiple victimisation experiences conferring greater risk for adverse mental health outcomes than does exposure to a single subtype. The application of latent class analysis (LCA) to child maltreatment has gained momentum, but it remains the case that few studies have incorporated a comprehensive range of subtypes, meaning that real-life patterns in victimisation experiences cannot be accurately modelled. Based on self-report data from an ethnically diverse sample (N = 2813) of 10-17 year olds in the United Kingdom, the current study used LCA to model constellations among nine types of maltreatment in the home (physical, emotional and sexual abuse; physical and emotional neglect; exposure to physical and verbal domestic violence, or a drug-related threat; and sibling violence). A four-class solution comprising of a low victimisation class (59.3% of participants), an emotional abuse and neglect class (19.0%), a high verbal domestic violence class (10.5%) and a maltreatment and domestic violence class (11.2%) provided the best fit for the data. Associations with sociodemographic variables were examined, revealing differences in the composition of the classes. Compared to the low victimisation class, participants in the verbal domestic violence class, emotional abuse and neglect class and especially the maltreatment and domestic violence class, reported higher symptoms of anxiety and depression and an increased likelihood of non-suicidal self-injury, suicide ideation and suicide attempt. The findings carry important implications for understanding patterns of child maltreatment, and the implications for preventative strategies and support services are discussed.
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Haroon S, Nirantharakumar K, Hughes SE, Subramanian A, Aiyegbusi OL, Davies EH, Myles P, Williams T, Turner G, Chandan JS, McMullan C, Lord J, Wraith DC, McGee K, Denniston AK, Taverner T, Jackson LJ, Sapey E, Gkoutos G, Gokhale K, Leggett E, Iles C, Frost C, McNamara G, Bamford A, Marshall T, Zemedikun DT, Price G, Marwaha S, Simms-Williams N, Brown K, Walker A, Jones K, Matthews K, Camaradou J, Saint-Cricq M, Kumar S, Alder Y, Stanton DE, Agyen L, Baber M, Blaize H, Calvert M. Therapies for Long COVID in non-hospitalised individuals: from symptoms, patient-reported outcomes and immunology to targeted therapies (The TLC Study). BMJ Open 2022; 12:e060413. [PMID: 35473737 PMCID: PMC9044550 DOI: 10.1136/bmjopen-2021-060413] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
INTRODUCTION Individuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies. METHODS AND ANALYSIS A cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink, and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability and patient-reported outcome measures. Data will be collected monthly for 1 year.Statistical clustering methods will be used to identify distinct Long COVID-19 symptom clusters. Individuals from the four most prevalent clusters and two control groups will be invited to participate in the BioWear substudy which will further phenotype Long COVID symptom clusters by measurement of immunological parameters and actigraphy.We will review existing evidence on interventions for postviral syndromes and Long COVID to map and prioritise interventions for each newly characterised Long COVID syndrome. Recommendations will be made using the cumulative evidence in an expert consensus workshop. A virtual supportive intervention will be coproduced with patients and health service providers for future evaluation.Individuals with lived experience of Long COVID will be involved throughout this programme through a patient and public involvement group. ETHICS AND DISSEMINATION Ethical approval was obtained from the Solihull Research Ethics Committee, West Midlands (21/WM/0203). Research findings will be presented at international conferences, in peer-reviewed journals, to Long COVID patient support groups and to policymakers. TRIAL REGISTRATION NUMBER 1567490.
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Affiliation(s)
- Shamil Haroon
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Krishnarajah Nirantharakumar
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- Health Data Research UK (HDR UK) Midlands, Birmingham, UK
| | - Sarah E Hughes
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- National Institute for Health Research (NIHR) Applied Research Centre West Midlands, Birmingham, UK
| | | | - Olalekan Lee Aiyegbusi
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- National Institute for Health Research (NIHR) Applied Research Centre West Midlands, Birmingham, UK
| | | | - Puja Myles
- Clinical Practice Research Datalink, Medicines and Healthcare Products Regulatory Agency, London, UK
| | - Tim Williams
- Clinical Practice Research Datalink, Medicines and Healthcare Products Regulatory Agency, London, UK
| | - Grace Turner
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Joht Singh Chandan
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Christel McMullan
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Janet Lord
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - David C Wraith
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Kirsty McGee
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | | | - Thomas Taverner
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Louise J Jackson
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Elizabeth Sapey
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - George Gkoutos
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Krishna Gokhale
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Edward Leggett
- Clinical Practice Research Datalink, Medicines and Healthcare Products Regulatory Agency, London, UK
| | - Clare Iles
- Clinical Practice Research Datalink, Medicines and Healthcare Products Regulatory Agency, London, UK
| | | | | | - Amy Bamford
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Tom Marshall
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Dawit T Zemedikun
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | | | - Steven Marwaha
- Institute for Mental Health, University of Birmingham, Birmingham, UK
| | | | - Kirsty Brown
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Anita Walker
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Karen Jones
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | | | | | | | | | | | | | | | | | | | - Melanie Calvert
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- Health Data Research UK (HDR UK) Midlands, Birmingham, UK
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Gardiner LJ, Carrieri AP, Bingham K, Macluskie G, Bunton D, McNeil M, Pyzer-Knapp EO. Combining explainable machine learning, demographic and multi-omic data to inform precision medicine strategies for inflammatory bowel disease. PLoS One 2022; 17:e0263248. [PMID: 35196350 PMCID: PMC8865677 DOI: 10.1371/journal.pone.0263248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/15/2022] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel diseases (IBDs), including ulcerative colitis and Crohn’s disease, affect several million individuals worldwide. These diseases are heterogeneous at the clinical, immunological and genetic levels and result from complex host and environmental interactions. Investigating drug efficacy for IBD can improve our understanding of why treatment response can vary between patients. We propose an explainable machine learning (ML) approach that combines bioinformatics and domain insight, to integrate multi-modal data and predict inter-patient variation in drug response. Using explanation of our models, we interpret the ML models’ predictions to infer unique combinations of important features associated with pharmacological responses obtained during preclinical testing of drug candidates in ex vivo patient-derived fresh tissues. Our inferred multi-modal features that are predictive of drug efficacy include multi-omic data (genomic and transcriptomic), demographic, medicinal and pharmacological data. Our aim is to understand variation in patient responses before a drug candidate moves forward to clinical trials. As a pharmacological measure of drug efficacy, we measured the reduction in the release of the inflammatory cytokine TNFα from the fresh IBD tissues in the presence/absence of test drugs. We initially explored the effects of a mitogen-activated protein kinase (MAPK) inhibitor; however, we later showed our approach can be applied to other targets, test drugs or mechanisms of interest. Our best model predicted TNFα levels from demographic, medicinal and genomic features with an error of only 4.98% on unseen patients. We incorporated transcriptomic data to validate insights from genomic features. Our results showed variations in drug effectiveness (measured by ex vivo assays) between patients that differed in gender, age or condition and linked new genetic polymorphisms to patient response variation to the anti-inflammatory treatment BIRB796 (Doramapimod). Our approach models IBD drug response while also identifying its most predictive features as part of a transparent ML precision medicine strategy.
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Affiliation(s)
- Laura-Jayne Gardiner
- IBM Research Europe—Daresbury, The Hartree Centre, Warrington, United Kingdom
- * E-mail: (APC); (LJG)
| | - Anna Paola Carrieri
- IBM Research Europe—Daresbury, The Hartree Centre, Warrington, United Kingdom
- * E-mail: (APC); (LJG)
| | - Karen Bingham
- REPROCELL Europe Ltd, Glasgow, Scotland, United Kingdom
| | | | - David Bunton
- REPROCELL Europe Ltd, Glasgow, Scotland, United Kingdom
| | - Marian McNeil
- Precision Medicine Scotland Innovation Centre, Teaching and Learning Building, Queen Elizabeth University Hospital, Glasgow, Scotland, United Kingdom
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Ejigu BA, Asfaw MD, Cavalerie L, Abebaw T, Nanyingi M, Baylis M. Assessing the impact of non-pharmaceutical interventions (NPI) on the dynamics of COVID-19: A mathematical modelling study of the case of Ethiopia. PLoS One 2021; 16:e0259874. [PMID: 34784379 PMCID: PMC8594814 DOI: 10.1371/journal.pone.0259874] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 10/28/2021] [Indexed: 12/23/2022] Open
Abstract
The World Health Organization (WHO) declared COVID-19 a pandemic on March 11, 2020 and by November 14, 2020 there were 53.3M confirmed cases and 1.3M reported deaths in the world. In the same period, Ethiopia reported 102K cases and 1.5K deaths. Effective public health preparedness and response to COVID-19 requires timely projections of the time and size of the peak of the outbreak. Currently, Ethiopia under the COVAX facility has begun vaccinating high risk populations but due to vaccine supply shortages and the absence of an effective treatment, the implementation of NPIs (non-pharmaceutical interventions), like hand washing, wearing face coverings or social distancing, still remain the most effective methods of controlling the pandemic as recommended by WHO. This study proposes a modified Susceptible Exposed Infected and Recovered (SEIR) model to predict the number of COVID-19 cases at different stages of the disease under the implementation of NPIs at different adherence levels in both urban and rural settings of Ethiopia. To estimate the number of cases and their peak time, 30 different scenarios were simulated. The results indicated that the peak time of the pandemic is different in urban and rural populations of Ethiopia. In the urban population, under moderate implementation of three NPIs the pandemic will be expected to reach its peak in December, 2020 with 147,972 cases, of which 18,100 are symptomatic and 957 will require admission to an Intensive Care Unit (ICU). Among the implemented NPIs, increasing the coverage of wearing masks by 10% could reduce the number of new cases on average by one-fifth in urban-populations. Varying the coverage of wearing masks in rural populations minimally reduces the number of cases. In conclusion, the models indicate that the projected number of hospital cases during the peak time is higher than the Ethiopian health system capacity. To contain symptomatic and ICU cases within the health system capacity, the government should pay attention to the strict implementation of the existing NPIs or impose additional public health measures.
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Affiliation(s)
- Bedilu Alamirie Ejigu
- Department of Statistics, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Manalebish Debalike Asfaw
- Department of Mathematics, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lisa Cavalerie
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Tilahun Abebaw
- Department of Mathematics, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mark Nanyingi
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Epidemiology and Public Health, School of Public Health, University of Nairobi, Nairobi, Kenya
| | - Matthew Baylis
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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43
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Ferrari M, Mekkaoui L, Ilca FT, Akbar Z, Bughda R, Lamb K, Ward K, Parekh F, Karattil R, Allen C, Wu P, Baldan V, Mattiuzzo G, Bentley EM, Takeuchi Y, Sillibourne J, Datta P, Kinna A, Pule M, Onuoha SC. Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. J Virol 2021; 95:e0068521. [PMID: 34287040 PMCID: PMC8432736 DOI: 10.1128/jvi.00685-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
The human angiotensin-converting enzyme 2 acts as the host cell receptor for SARS-CoV-2 and the other members of the Coronaviridae family SARS-CoV-1 and HCoV-NL63. Here, we report the biophysical properties of the SARS-CoV-2 spike variants D614G, B.1.1.7, B.1.351, and P.1 with affinities to the ACE2 receptor and infectivity capacity, revealing weaknesses in the developed neutralizing antibody approaches. Furthermore, we report a preclinical characterization package for a soluble receptor decoy engineered to be catalytically inactive and immunologically inert, with broad neutralization capacity, that represents an attractive therapeutic alternative in light of the mutational landscape of COVID-19. This construct efficiently neutralized four SARS-CoV-2 variants of concern. The decoy also displays antibody-like biophysical properties and manufacturability, strengthening its suitability as a first-line treatment option in prophylaxis or therapeutic regimens for COVID-19 and related viral infections. IMPORTANCE Mutational drift of SARS-CoV-2 risks rendering both therapeutics and vaccines less effective. Receptor decoy strategies utilizing soluble human ACE2 may overcome the risk of viral mutational escape since mutations disrupting viral interaction with the ACE2 decoy will by necessity decrease virulence, thereby preventing meaningful escape. The solution described here of a soluble ACE2 receptor decoy is significant for the following reasons: while previous ACE2-based therapeutics have been described, ours has novel features, including (i) mutations within ACE2 to remove catalytical activity and systemic interference with the renin/angiotensin system, (ii) abrogated FcγR engagement, reduced risk of antibody-dependent enhancement of infection, and reduced risk of hyperinflammation, and (iii) streamlined antibody-like purification process and scale-up manufacturability indicating that this receptor decoy could be produced quickly and easily at scale. Finally, we demonstrate that ACE2-based therapeutics confer a broad-spectrum neutralization potency for ACE2-tropic viruses, including SARS-CoV-2 variants of concern in contrast to therapeutic MAb.
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Affiliation(s)
| | | | - F Tudor Ilca
- Autolus Limited, The MediaWorks, London, United Kingdom
| | | | - Reyisa Bughda
- Autolus Limited, The MediaWorks, London, United Kingdom
| | - Katarina Lamb
- Autolus Limited, The MediaWorks, London, United Kingdom
| | | | | | | | | | - Philip Wu
- Autolus Limited, The MediaWorks, London, United Kingdom
| | - Vania Baldan
- Autolus Limited, The MediaWorks, London, United Kingdom
| | - Giada Mattiuzzo
- National Institute for Biological Standards and Controlgrid.70909.37, Herts, United Kingdom
| | - Emma M Bentley
- National Institute for Biological Standards and Controlgrid.70909.37, Herts, United Kingdom
| | - Yasuhiro Takeuchi
- National Institute for Biological Standards and Controlgrid.70909.37, Herts, United Kingdom
- Division of Infection and Immunity, University College Londongrid.83440.3b, London, United Kingdom
| | | | - Preeta Datta
- Autolus Limited, The MediaWorks, London, United Kingdom
| | | | - Martin Pule
- Autolus Limited, The MediaWorks, London, United Kingdom
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Carnell GW, Ciazynska KA, Wells DA, Xiong X, Aguinam ET, McLaughlin SH, Mallery D, Ebrahimi S, Ceron-Gutierrez L, Asbach B, Einhauser S, Wagner R, James LC, Doffinger R, Heeney JL, Briggs JAG. SARS-CoV-2 Spike Protein Stabilized in the Closed State Induces Potent Neutralizing Responses. J Virol 2021; 95:e0020321. [PMID: 33963055 PMCID: PMC8274612 DOI: 10.1128/jvi.00203-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
The majority of SARS-CoV-2 vaccines in use or advanced development are based on the viral spike protein (S) as their immunogen. S is present on virions as prefusion trimers in which the receptor binding domain (RBD) is stochastically open or closed. Neutralizing antibodies have been described against both open and closed conformations. The long-term success of vaccination strategies depends upon inducing antibodies that provide long-lasting broad immunity against evolving SARS-CoV-2 strains. Here, we have assessed the results of immunization in a mouse model using an S protein trimer stabilized in the closed state to prevent full exposure of the receptor binding site and therefore interaction with the receptor. We compared this with other modified S protein constructs, including representatives used in current vaccines. We found that all trimeric S proteins induced a T cell response and long-lived, strongly neutralizing antibody responses against 2019 SARS-CoV-2 and variants of concern P.1 and B.1.351. Notably, the protein binding properties of sera induced by the closed spike differed from those induced by standard S protein constructs. Closed S proteins induced more potent neutralizing responses than expected based on the degree to which they inhibit interactions between the RBD and ACE2. These observations suggest that closed spikes recruit different, but equally potent, immune responses than open spikes and that this is likely to include neutralizing antibodies against conformational epitopes present in the closed conformation. We suggest that closed spikes, together with their improved stability and storage properties, may be a valuable component of refined, next-generation vaccines. IMPORTANCE Vaccines in use against SARS-CoV-2 induce immune responses against the spike protein. There is intense interest in whether the antibody response induced by vaccines will be robust against new variants, as well as in next-generation vaccines for use in previously infected or immunized individuals. We assessed the use as an immunogen of a spike protein engineered to be conformationally stabilized in the closed state where the receptor binding site is occluded. Despite occlusion of the receptor binding site, the spike induces potently neutralizing sera against multiple SARS-CoV-2 variants. Antibodies are raised against a different pattern of epitopes to those induced by other spike constructs, preferring conformational epitopes present in the closed conformation. Closed spikes, or mRNA vaccines based on their sequence, can be a valuable component of next-generation vaccines.
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Affiliation(s)
- George W. Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - David A. Wells
- DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - Xiaoli Xiong
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ernest T. Aguinam
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Donna Mallery
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Soraya Ebrahimi
- Department of Clinical Biochemistry and Immunology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Lourdes Ceron-Gutierrez
- Department of Clinical Biochemistry and Immunology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Benedikt Asbach
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Sebastian Einhauser
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Leo C. James
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Jonathan L. Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- DIOSynVax, University of Cambridge, Cambridge, United Kingdom
| | - John A. G. Briggs
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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Wang W, Baker M, Hu Y, Xu J, Yang D, Maciel-Guerra A, Xue N, Li H, Yan S, Li M, Bai Y, Dong Y, Peng Z, Ma J, Li F, Dottorini T. Whole-Genome Sequencing and Machine Learning Analysis of Staphylococcus aureus from Multiple Heterogeneous Sources in China Reveals Common Genetic Traits of Antimicrobial Resistance. mSystems 2021; 6:e0118520. [PMID: 34100643 PMCID: PMC8579812 DOI: 10.1128/msystems.01185-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/10/2021] [Indexed: 12/27/2022] Open
Abstract
Staphylococcus aureus is a worldwide leading cause of numerous diseases ranging from food-poisoning to lethal infections. Methicillin-resistant S. aureus (MRSA) has been found capable of acquiring resistance to most antimicrobials. MRSA is ubiquitous and diverse even in terms of antimicrobial resistance (AMR) profiles, posing a challenge for treatment. Here, we present a comprehensive study of S. aureus in China, addressing epidemiology, phylogenetic reconstruction, genomic characterization, and identification of AMR profiles. The study analyzes 673 S. aureus isolates from food as well as from hospitalized and healthy individuals. The isolates have been collected over a 9-year period, between 2010 and 2018, from 27 provinces across China. By whole-genome sequencing, Bayesian divergence analysis, and supervised machine learning, we reconstructed the phylogeny of the isolates and compared them to references from other countries. We identified 72 sequence types (STs), of which, 29 were novel. We found 81 MRSA lineages by multilocus sequence type (MLST), spa, staphylococcal cassette chromosome mec element (SCCmec), and Panton-Valentine leukocidin (PVL) typing. In addition, novel variants of SCCmec type IV hosting extra metal and antimicrobial resistance genes, as well as a new SCCmec type, were found. New Bayesian dating of the split times of major clades showed that ST9, ST59, and ST239 in China and European countries fell in different branches, whereas this pattern was not observed for the ST398 clone. On the contrary, the clonal transmission of ST398 was more intermixed in regard to geographic origin. Finally, we identified genetic determinants of resistance to 10 antimicrobials, discriminating drug-resistant bacteria from susceptible strains in the cohort. Our results reveal the emergence of Chinese MRSA lineages enriched of AMR determinants that share similar genetic traits of antimicrobial resistance across human and food, hinting at a complex scenario of evolving transmission routes. IMPORTANCE Little information is available on the epidemiology and characterization of Staphylococcus aureus in China. The role of food is a cause of major concern: staphylococcal foodborne diseases affect thousands every year, and the presence of resistant Staphylococcus strains on raw retail meat products is well documented. We studied a large heterogeneous data set of S. aureus isolates from many provinces of China, isolated from food as well as from individuals. Our large whole-genome collection represents a unique catalogue that can be easily meta-analyzed and integrated with further studies and adds to the library of S. aureus sequences in the public domain in a currently underrepresented geographical region. The new Bayesian dating of the split times of major drug-resistant enriched clones is relevant in showing that Chinese and European methicillin-resistant S. aureus (MRSA) have evolved differently. Our machine learning approach, across a large number of antibiotics, shows novel determinants underlying resistance and reveals frequent resistant traits in specific clonal complexes, highlighting the importance of particular clonal complexes in China. Our findings substantially expand what is known of the evolution and genetic determinants of resistance in food-associated S. aureus in China and add crucial information for whole-genome sequencing (WGS)-based surveillance of S. aureus.
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Affiliation(s)
- Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Dajin Yang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | | | - Ning Xue
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
| | - Hui Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Shaofei Yan
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Menghan Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Yao Bai
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Jinjing Ma
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
- School of Chemistry and Chemical Engineering, Anqing Normal University, Anqing, Anhui, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
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46
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Clements AL, Sealy JE, Peacock TP, Sadeyen JR, Hussain S, Lycett SJ, Shelton H, Digard P, Iqbal M. Contribution of Segment 3 to the Acquisition of Virulence in Contemporary H9N2 Avian Influenza Viruses. J Virol 2020; 94:e01173-20. [PMID: 32727875 PMCID: PMC7527061 DOI: 10.1128/jvi.01173-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 06/09/2020] [Accepted: 07/27/2020] [Indexed: 12/16/2022] Open
Abstract
H9N2 avian influenza viruses (AIVs) circulate in poultry throughout much of Asia, the Middle East, and Africa. These viruses cause huge economic damage to poultry production systems and pose a zoonotic threat both in their own right and in the generation of novel zoonotic viruses, for example, H7N9. In recent years, it has been observed that H9N2 viruses have further adapted to gallinaceous poultry, becoming more highly transmissible and causing higher morbidity and mortality. Here, we investigate the molecular basis for this increased virulence, comparing a virus from the 1990s and a contemporary field strain. The modern virus replicated to higher titers in various systems, and this difference mapped to a single amino acid polymorphism at position 26 of the endonuclease domain shared by the PA and PA-X proteins. This change was responsible for increased replication and higher morbidity and mortality rates along with extended tissue tropism seen in chickens. Although the PA K26E change correlated with increased host cell shutoff activity of the PA-X protein in vitro, it could not be overridden by frameshift site mutations that block PA-X expression and therefore increased PA-X activity could not explain the differences in replication phenotype. Instead, this indicates that these differences are due to subtle effects on PA function. This work gives insight into the ongoing evolution and poultry adaptation of H9N2 and other avian influenza viruses and helps us understand the striking morbidity and mortality rates in the field, as well as the rapidly expanding geographical range seen in these viruses.IMPORTANCE Avian influenza viruses, such as H9N2, cause huge economic damage to poultry production worldwide and are additionally considered potential pandemic threats. Understanding how these viruses evolve in their natural hosts is key to effective control strategies. In the Middle East and South Asia, an older H9N2 virus strain has been replaced by a new reassortant strain with greater fitness. Here, we take representative viruses and investigate the genetic basis for this "fitness." A single mutation in the virus was responsible for greater fitness, enabling high growth of the contemporary H9N2 virus in cells, as well as in chickens. The genetic mutation that modulates this change is within the viral PA protein, a part of the virus polymerase gene that contributes to viral replication as well as to virus accessory functions-however, we find that the fitness effect is specifically due to changes in the protein polymerase activity.
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Affiliation(s)
- Anabel L Clements
- The Pirbright Institute, Pirbright, Woking, United Kingdom
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Joshua E Sealy
- The Pirbright Institute, Pirbright, Woking, United Kingdom
| | - Thomas P Peacock
- The Pirbright Institute, Pirbright, Woking, United Kingdom
- Department of Infectious Diseases, Imperial College London, United Kingdom
| | | | - Saira Hussain
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Samantha J Lycett
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Holly Shelton
- The Pirbright Institute, Pirbright, Woking, United Kingdom
| | - Paul Digard
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Munir Iqbal
- The Pirbright Institute, Pirbright, Woking, United Kingdom
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