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Arsevska E, Hengl T, Singleton DA, Noble PJM, Caminade C, Eneanya OA, Jones PH, Medlock JM, Hansford KM, Bonannella C, Radford AD. Risk factors for tick attachment in companion animals in Great Britain: a spatiotemporal analysis covering 2014-2021. Parasit Vectors 2024; 17:29. [PMID: 38254168 PMCID: PMC10804489 DOI: 10.1186/s13071-023-06094-4] [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: 06/30/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Ticks are an important driver of veterinary health care, causing irritation and sometimes infection to their hosts. We explored epidemiological and geo-referenced data from > 7 million electronic health records (EHRs) from cats and dogs collected by the Small Animal Veterinary Surveillance Network (SAVSNET) in Great Britain (GB) between 2014 and 2021 to assess the factors affecting tick attachment in an individual and at a spatiotemporal level. METHODS EHRs in which ticks were mentioned were identified by text mining; domain experts confirmed those with ticks on the animal. Tick presence/absence records were overlaid with a spatiotemporal series of climate, environment, anthropogenic and host distribution factors to produce a spatiotemporal regression matrix. An ensemble machine learning spatiotemporal model was used to fine-tune hyperparameters for Random Forest, Gradient-boosted Trees and Generalized Linear Model regression algorithms, which were then used to produce a final ensemble meta-learner to predict the probability of tick attachment across GB at a monthly interval and averaged long-term through 2014-2021 at a spatial resolution of 1 km. Individual host factors associated with tick attachment were also assessed by conditional logistic regression on a matched case-control dataset. RESULTS In total, 11,741 consultations were identified in which a tick was recorded. The frequency of tick records was low (0.16% EHRs), suggesting an underestimation of risk. That said, increased odds for tick attachment in cats and dogs were associated with younger adult ages, longer coat length, crossbreeds and unclassified breeds. In cats, males and entire animals had significantly increased odds of recorded tick attachment. The key variables controlling the spatiotemporal risk for tick attachment were climatic (precipitation and temperature) and vegetation type (Enhanced Vegetation Index). Suitable areas for tick attachment were predicted across GB, especially in forests and grassland areas, mainly during summer, particularly in June. CONCLUSIONS Our results can inform targeted health messages to owners and veterinary practitioners, identifying those animals, seasons and areas of higher risk for tick attachment and allowing for more tailored prophylaxis to reduce tick burden, inappropriate parasiticide treatment and potentially TBDs in companion animals and humans. Sentinel networks like SAVSNET represent a novel complementary data source to improve our understanding of tick attachment risk for companion animals and as a proxy of risk to humans.
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Affiliation(s)
- Elena Arsevska
- Unit for Animals, Health, Territories, Risks and Ecosystems (UMR ASTRE), French Agricultural Research Centre for International Development (CIRAD), 34980, Montferrier-sur-Lez, France.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, CH64 7TE, Neston, UK.
| | - Tomislav Hengl
- OpenGeoHub Foundation, 6708 PW, Wageningen, The Netherlands
| | - David A Singleton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, CH64 7TE, Neston, UK
| | - Peter-John M Noble
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, CH64 7TE, Neston, UK
| | - Cyril Caminade
- Earth System Physics Department, Abdus Salam International Centre for Theoretical Physics (ICTP), 34151, Trieste, Italy
| | - Obiora A Eneanya
- Health Programs, The Carter Center, 30307, Atlanta, Georgia, USA
| | - Philip H Jones
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, CH64 7TE, Neston, UK
| | - Jolyon M Medlock
- Medical Entomology and Zoonoses Ecology, UK Health Security Agency, SP4 0JG, Salisbury, UK
- NIHR Health Protection Research Unit in Environmental Change and Health, WC1E 7HT, London, UK
| | - Kayleigh M Hansford
- Medical Entomology and Zoonoses Ecology, UK Health Security Agency, SP4 0JG, Salisbury, UK
- NIHR Health Protection Research Unit in Environmental Change and Health, WC1E 7HT, London, UK
| | - Carmelo Bonannella
- OpenGeoHub Foundation, 6708 PW, Wageningen, The Netherlands
- Laboratory of Geo-information Science and Remote Sensing, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
| | - Alan D Radford
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, CH64 7TE, Neston, UK
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2
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Olafsson S, Rodriguez E, Lawson ARJ, Abascal F, Huber AR, Suembuel M, Jones PH, Gerdes S, Martincorena I, Weidinger S, Campbell PJ, Anderson CA. Effects of psoriasis and psoralen exposure on the somatic mutation landscape of the skin. Nat Genet 2023; 55:1892-1900. [PMID: 37884686 PMCID: PMC10632143 DOI: 10.1038/s41588-023-01545-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/20/2023] [Indexed: 10/28/2023]
Abstract
Somatic mutations are hypothesized to play a role in many non-neoplastic diseases. We performed whole-exome sequencing of 1,182 microbiopsies dissected from lesional and nonlesional epidermis from 111 patients with psoriasis to search for evidence that somatic mutations in keratinocytes may influence the disease process. Lesional skin remained highly polyclonal, showing no evidence of large-scale spread of clones carrying potentially pathogenic mutations. The mutation rate of keratinocytes was similarly only modestly affected by the disease. We found evidence of positive selection in previously reported driver genes NOTCH1, NOTCH2, TP53, FAT1 and PPM1D and also identified mutations in four genes (GXYLT1, CHEK2, ZFP36L2 and EEF1A1) that we hypothesize are selected for in squamous epithelium irrespective of disease status. Finally, we describe a mutational signature of psoralens-a class of chemicals previously found in some sunscreens and which are used as part of PUVA (psoralens and ultraviolet-A) photochemotherapy treatment for psoriasis.
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Affiliation(s)
| | - Elke Rodriguez
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | | | | | - Melike Suembuel
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Sascha Gerdes
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Stephan Weidinger
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
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Treger TD, Lawrence JEG, Anderson ND, Coorens THH, Letunovska A, Abby E, Lee-Six H, Oliver TRW, Al-Saadi R, Tullus K, Morcrette G, Hutchinson JC, Rampling D, Sebire N, Pritchard-Jones K, Young MD, Mitchell TJ, Jones PH, Tran M, Behjati S, Chowdhury T. Targetable NOTCH1 rearrangements in reninoma. Nat Commun 2023; 14:5826. [PMID: 37749094 PMCID: PMC10519988 DOI: 10.1038/s41467-023-41118-8] [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: 11/22/2022] [Accepted: 08/23/2023] [Indexed: 09/27/2023] Open
Abstract
Reninomas are exceedingly rare renin-secreting kidney tumours that derive from juxtaglomerular cells, specialised smooth muscle cells that reside at the vascular inlet of glomeruli. They are the central component of the juxtaglomerular apparatus which controls systemic blood pressure through the secretion of renin. We assess somatic changes in reninoma and find structural variants that generate canonical activating rearrangements of, NOTCH1 whilst removing its negative regulator, NRARP. Accordingly, in single reninoma nuclei we observe excessive renin and NOTCH1 signalling mRNAs, with a concomitant non-excess of NRARP expression. Re-analysis of previously published reninoma bulk transcriptomes further corroborates our observation of dysregulated Notch pathway signalling in reninoma. Our findings reveal NOTCH1 rearrangements in reninoma, therapeutically targetable through existing NOTCH1 inhibitors, and indicate that unscheduled Notch signalling may be a disease-defining feature of reninoma.
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Affiliation(s)
- Taryn D Treger
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - John E G Lawrence
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | | | - Tim H H Coorens
- Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA
| | - Aleksandra Letunovska
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | - Emilie Abby
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Henry Lee-Six
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Reem Al-Saadi
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | - Kjell Tullus
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | - Guillaume Morcrette
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | - J Ciaran Hutchinson
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | - Dyanne Rampling
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | - Neil Sebire
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | | | | | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Early Cancer Institute, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Oncology, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Maxine Tran
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London, NW3 2QG, UK.
- Faculty of Medical Sciences, Division of Surgery and Interventional Science, University College London, London, NW3 2PS, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
| | - Tanzina Chowdhury
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK.
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK.
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King C, Fowler JC, Abnizova I, Sood RK, Hall MWJ, Szeverényi I, Tham M, Huang J, Young SM, Hall BA, Birgitte Lane E, Jones PH. Author Correction: Somatic mutations in facial skin from countries of contrasting skin cancer risk. Nat Genet 2023; 55:1608. [PMID: 37626225 PMCID: PMC10484781 DOI: 10.1038/s41588-023-01508-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Affiliation(s)
| | | | | | | | - Michael W J Hall
- Wellcome Sanger Institute, Hinxton, UK
- Department of Oncology, University of Cambridge, Hutchinson Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Ildikó Szeverényi
- Skin Research Institute of Singapore and Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Institute of Aquaculture and Environmental Safety, Georgikon Campus, Hungarian University of Agricultural and Life Sciences, Keszthely, Hungary
| | - Muly Tham
- Skin Research Institute of Singapore and Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jingxiang Huang
- Skin Research Institute of Singapore and Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - E Birgitte Lane
- Skin Research Institute of Singapore and Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, UK.
- Department of Oncology, University of Cambridge, Hutchinson Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
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5
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King C, Fowler JC, Abnizova I, Sood RK, Hall MWJ, Szeverényi I, Tham M, Huang J, Young SM, Hall BA, Birgitte Lane E, Jones PH. Somatic mutations in facial skin from countries of contrasting skin cancer risk. Nat Genet 2023; 55:1440-1447. [PMID: 37537257 PMCID: PMC10484783 DOI: 10.1038/s41588-023-01468-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
Abstract
The incidence of keratinocyte cancer (basal cell and squamous cell carcinomas of the skin) is 17-fold lower in Singapore than the UK1-3, despite Singapore receiving 2-3 times more ultraviolet (UV) radiation4,5. Aging skin contains somatic mutant clones from which such cancers develop6,7. We hypothesized that differences in keratinocyte cancer incidence may be reflected in the normal skin mutational landscape. Here we show that, compared to Singapore, aging facial skin from populations in the UK has a fourfold greater mutational burden, a predominant UV mutational signature, increased copy number aberrations and increased mutant TP53 selection. These features are shared by keratinocyte cancers from high-incidence and low-incidence populations8-13. In Singaporean skin, most mutations result from cell-intrinsic processes; mutant NOTCH1 and NOTCH2 are more strongly selected than in the UK. Aging skin in a high-incidence country has multiple features convergent with cancer that are not found in a low-risk country. These differences may reflect germline variation in UV-protective genes.
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Affiliation(s)
| | | | | | | | - Michael W J Hall
- Wellcome Sanger Institute, Hinxton, UK
- Department of Oncology, University of Cambridge, Hutchinson Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Ildikó Szeverényi
- Skin Research Institute of Singapore and Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Institute of Aquaculture and Environmental Safety, Georgikon Campus, Hungarian University of Agricultural and Life Sciences, Keszthely, Hungary
| | - Muly Tham
- Skin Research Institute of Singapore and Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jingxiang Huang
- Skin Research Institute of Singapore and Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - E Birgitte Lane
- Skin Research Institute of Singapore and Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, UK.
- Department of Oncology, University of Cambridge, Hutchinson Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
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6
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Hall MWJ, Shorthouse D, Alcraft R, Jones PH, Hall BA. Mutations observed in somatic evolution reveal underlying gene mechanisms. Commun Biol 2023; 6:753. [PMID: 37468606 PMCID: PMC10356810 DOI: 10.1038/s42003-023-05136-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023] Open
Abstract
Highly sensitive DNA sequencing techniques have allowed the discovery of large numbers of somatic mutations in normal tissues. Some mutations confer a competitive advantage over wild-type cells, generating expanding clones that spread through the tissue. Competition between mutant clones leads to selection. This process can be considered a large scale, in vivo screen for mutations increasing cell fitness. It follows that somatic missense mutations may offer new insights into the relationship between protein structure, function and cell fitness. We present a flexible statistical method for exploring the selection of structural features in data sets of somatic mutants. We show how this approach can evidence selection of specific structural features in key drivers in aged tissues. Finally, we show how drivers may be classified as fitness-enhancing and fitness-suppressing through different patterns of mutation enrichment. This method offers a route to understanding the mechanism of protein function through in vivo mutant selection.
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Affiliation(s)
| | - David Shorthouse
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London, WC1E 6BT, UK
| | - Rachel Alcraft
- Advanced Research Computing, University College London, London, UK
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Oncology, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London, WC1E 6BT, UK.
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7
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Herms A, Jones PH. Somatic Mutations in Normal Tissues: New Perspectives on Early Carcinogenesis. Annu Rev Cancer Biol 2023. [DOI: 10.1146/annurev-cancerbio-061421-012447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Normal tissues progressively acquire mutations. Some mutations are positively selected, driving clonal expansions that may colonize the majority of a tissue by old age. In several cases mutant clonal expansion is due to biasing stem cell fate toward proliferation. However, the expansionary phase is transient and is followed by reversion toward wild-type behavior so that normal tissue integrity is retained. Here we consider the implications of these findings for carcinogenesis. We propose that to be considered a cancer driver, a mutant gene should be more prevalent in tumors than the normal lineage from which it emerged. Cancer risk is not dependent on mutational burden, but rather may reflect the relative frequency of pro- and anti-oncogenic mutants within a tissue. Understanding the basis of mutant clonal advantage over wild-type cells allows interventions to halt the expansion or even deplete oncogenic mutants from normal tissue, potentially lowering cancer risk. Expected final online publication date for the Annual Review of Cancer Biology, Volume 7 is April 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Albert Herms
- Department of Biomedical Sciences, Faculty of Medicine, Universitat de Barcelona, Barcelona, Spain
- Cell Compartments and Signaling Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Philip H. Jones
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Oncology, University of Cambridge, Hutchinson Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
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Abby E, Dentro SC, Hall MWJ, Fowler JC, Ong SH, Sood R, Herms A, Piedrafita G, Abnizova I, Siebel CW, Gerstung M, Hall BA, Jones PH. Notch1 mutations drive clonal expansion in normal esophageal epithelium but impair tumor growth. Nat Genet 2023; 55:232-245. [PMID: 36658434 PMCID: PMC9925379 DOI: 10.1038/s41588-022-01280-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 12/07/2022] [Indexed: 01/21/2023]
Abstract
NOTCH1 mutant clones occupy the majority of normal human esophagus by middle age but are comparatively rare in esophageal cancers, suggesting NOTCH1 mutations drive clonal expansion but impede carcinogenesis. Here we test this hypothesis. Sequencing NOTCH1 mutant clones in aging human esophagus reveals frequent biallelic mutations that block NOTCH1 signaling. In mouse esophagus, heterozygous Notch1 mutation confers a competitive advantage over wild-type cells, an effect enhanced by loss of the second allele. Widespread Notch1 loss alters transcription but has minimal effects on the epithelial structure and cell dynamics. In a carcinogenesis model, Notch1 mutations were less prevalent in tumors than normal epithelium. Deletion of Notch1 reduced tumor growth, an effect recapitulated by anti-NOTCH1 antibody treatment. Notch1 null tumors showed reduced proliferation. We conclude that Notch1 mutations in normal epithelium are beneficial as wild-type Notch1 favors tumor expansion. NOTCH1 blockade may have therapeutic potential in preventing esophageal squamous cancer.
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Affiliation(s)
| | - Stefan C Dentro
- Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- Artificial Intelligence in Oncology (B450), Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Michael W J Hall
- Wellcome Sanger Institute, Hinxton, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | | | | | | | - Albert Herms
- Wellcome Sanger Institute, Hinxton, UK
- Department of Biomedical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Gabriel Piedrafita
- Department of Biochemistry and Molecular Biology, Complutense University, Madrid, Spain
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Christian W Siebel
- Department of Discovery Oncology, Genentech, South San Francisco, CA, USA
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- Artificial Intelligence in Oncology (B450), Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
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9
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Tognato R, Jones PH. Ray Optics Model for Optical Trapping of Biconcave Red Blood Cells. Micromachines (Basel) 2022; 14:mi14010083. [PMID: 36677144 PMCID: PMC9867239 DOI: 10.3390/mi14010083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 05/28/2023]
Abstract
Red blood cells (RBCs) or erythrocytes are essential for oxygenating the peripherical tissue in the human body. Impairment of their physical properties may lead to severe diseases. Optical tweezers have in experiments been shown to be a powerful tool for assessing the biochemical and biophysical properties of RBCs. Despite this success there has been little theoretical work investigating of the stability of erythrocytes in optical tweezers. In this paper we report a numerical study of the trapping of RBCs in the healthy, native biconcave disk conformation in optical tweezers using the ray optics approximation. We study trapping using both single- and dual-beam optical tweezers and show that the complex biconcave shape of the RBC is a significant factor in determining the optical forces and torques on the cell, and ultimately the equilibrium configuration of the RBC within the trap. We also numerically demonstrate how the addition of a third or even fourth trapping laser beam can be used to control the cell orientation in the optical trap. The present investigation sheds light on the trapping mechanism of healthy erythrocytes and can be exploited by experimentalist to envisage new experiments.
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Herms A, Jones PH. Splitting up differentiation and cell cycle exit. Nat Cell Biol 2022; 24:1687-1688. [PMID: 36357620 DOI: 10.1038/s41556-022-01022-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Albert Herms
- Department of Biomedical Sciences, Faculty of Medicine, Universitat de Barcelona, Barcelona, Spain.,Cell Compartments and Signalling Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, UK. .,Department of Oncology, University of Cambridge, Hutchison Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
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Murai K, Dentro S, Ong SH, Sood R, Fernandez-Antoran D, Herms A, Kostiou V, Abnizova I, Hall BA, Gerstung M, Jones PH. p53 mutation in normal esophagus promotes multiple stages of carcinogenesis but is constrained by clonal competition. Nat Commun 2022; 13:6206. [PMID: 36266286 PMCID: PMC9584949 DOI: 10.1038/s41467-022-33945-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/07/2022] [Indexed: 02/02/2023] Open
Abstract
Aging normal human oesophagus accumulates TP53 mutant clones. These are the origin of most oesophageal squamous carcinomas, in which biallelic TP53 disruption is almost universal. However, how p53 mutant clones expand and contribute to cancer development is unclear. Here we show that inducing the p53R245W mutant in single oesophageal progenitor cells in transgenic mice confers a proliferative advantage and clonal expansion but does not disrupt normal epithelial structure. Loss of the remaining p53 allele in mutant cells results in genomically unstable p53R245W/null epithelium with giant polyaneuploid cells and copy number altered clones. In carcinogenesis, p53 mutation does not initiate tumour formation, but tumours developing from areas with p53 mutation and LOH are larger and show extensive chromosomal instability compared to lesions arising in wild type epithelium. We conclude that p53 has distinct functions at different stages of carcinogenesis and that LOH within p53 mutant clones in normal epithelium is a critical step in malignant transformation.
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Affiliation(s)
- Kasumi Murai
- Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Stefan Dentro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom
- DKFZ, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Roshan Sood
- Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - David Fernandez-Antoran
- Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
- Wellcome/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Road, Cambridge, CB2 1QN, United Kingdom
| | - Albert Herms
- Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Vasiliki Kostiou
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Irina Abnizova
- Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom
- DKFZ, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom.
- Department of Oncology, University of Cambridge, Cambridge, UK.
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12
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Fowler JC, Jones PH. Somatic mutation: What shapes the mutational landscape of normal epithelia? Cancer Discov 2022; 12:1642-1655. [PMID: 35397477 DOI: 10.1158/2159-8290.cd-22-0145] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/11/2022] [Accepted: 04/01/2022] [Indexed: 11/16/2022]
Abstract
Epithelial stem cells accumulate mutations throughout life. Some of these mutants increase competitive fitness and may form clones that colonize the stem cell niche and persist to acquire further genome alterations. After a transient expansion, mutant stem cells must revert to homeostatic behavior so normal tissue architecture is maintained. Some positively selected mutants may promote cancer development while others inhibit carcinogenesis. Factors that shape the mutational landscape include wild type and mutant stem cell dynamics, competition for the niche, and environmental exposures. Understanding these processes may give new insight into the basis of cancer risk and opportunities for cancer prevention.
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13
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Chen H, Lin H, Jones PH, Chen Z, Luo S, Pu J. Influence of slow light effect on trapping force in optical tweezers. Opt Lett 2022; 47:710-713. [PMID: 35103714 DOI: 10.1364/ol.448727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
We investigate the optical trapping of polystyrene microspheres in optical tweezers. The transverse capture gradient forces of polystyrene microspheres with different numerical aperture are theoretically and experimentally evaluated by the power spectral density roll-off method. It is found that the trapping force of the experimental measurement is much stronger than that of the theoretical results. The discordance is attributed to the slow light effect near the focus, which has been found in recent years [Science347, 857 (2015)10.1126/science.aaa3035; Opt. Express18, 10822 (2010)10.1364/OE.18.010822; Opt. Commun.332, 164 (2014)10.1016/j.optcom.2014.06.057]. The modified trapping force of the theoretical results by considering the slow light effect near the focus is well consistent with that of the experimental results.
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14
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Colom B, Herms A, Hall MWJ, Dentro SC, King C, Sood RK, Alcolea MP, Piedrafita G, Fernandez-Antoran D, Ong SH, Fowler JC, Mahbubani KT, Saeb-Parsy K, Gerstung M, Hall BA, Jones PH. Mutant clones in normal epithelium outcompete and eliminate emerging tumours. Nature 2021; 598:510-514. [PMID: 34646013 PMCID: PMC7612642 DOI: 10.1038/s41586-021-03965-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [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: 08/03/2020] [Accepted: 08/26/2021] [Indexed: 02/08/2023]
Abstract
Human epithelial tissues accumulate cancer-driver mutations with age1-9, yet tumour formation remains rare. The positive selection of these mutations suggests that they alter the behaviour and fitness of proliferating cells10-12. Thus, normal adult tissues become a patchwork of mutant clones competing for space and survival, with the fittest clones expanding by eliminating their less competitive neighbours11-14. However, little is known about how such dynamic competition in normal epithelia influences early tumorigenesis. Here we show that the majority of newly formed oesophageal tumours are eliminated through competition with mutant clones in the adjacent normal epithelium. We followed the fate of nascent, microscopic, pre-malignant tumours in a mouse model of oesophageal carcinogenesis and found that most were rapidly lost with no indication of tumour cell death, decreased proliferation or an anti-tumour immune response. However, deep sequencing of ten-day-old and one-year-old tumours showed evidence of selection on the surviving neoplasms. Induction of highly competitive clones in transgenic mice increased early tumour removal, whereas pharmacological inhibition of clonal competition reduced tumour loss. These results support a model in which survival of early neoplasms depends on their competitive fitness relative to that of mutant clones in the surrounding normal tissue. Mutant clones in normal epithelium have an unexpected anti-tumorigenic role in purging early tumours through cell competition, thereby preserving tissue integrity.
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Affiliation(s)
- B Colom
- Wellcome Sanger Institute, Hinxton, UK
| | - A Herms
- Wellcome Sanger Institute, Hinxton, UK
| | - M W J Hall
- Wellcome Sanger Institute, Hinxton, UK
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge, UK
| | - S C Dentro
- Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - C King
- Wellcome Sanger Institute, Hinxton, UK
| | - R K Sood
- Wellcome Sanger Institute, Hinxton, UK
| | - M P Alcolea
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Hutchison-MRC Research Centre, Cambridge, UK
| | - G Piedrafita
- Wellcome Sanger Institute, Hinxton, UK
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - D Fernandez-Antoran
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome Trust-Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - S H Ong
- Wellcome Sanger Institute, Hinxton, UK
| | | | - K T Mahbubani
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - K Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - M Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - B A Hall
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - P H Jones
- Wellcome Sanger Institute, Hinxton, UK.
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge, UK.
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15
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Kostiou V, Hall MWJ, Jones PH, Hall BA. Simulations reveal that different responses to cell crowding determine the expansion of p53 and Notch mutant clones in squamous epithelia. J R Soc Interface 2021; 18:20210607. [PMID: 34637643 PMCID: PMC8510697 DOI: 10.1098/rsif.2021.0607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/16/2021] [Indexed: 12/31/2022] Open
Abstract
During ageing, normal epithelial tissues progressively accumulate clones carrying mutations that increase mutant cell fitness above that of wild-type cells. Such mutants spread widely through the tissues, yet despite this cellular homeostasis and functional integrity of the epithelia are maintained. Two of the genes most commonly mutated in human skin and oesophagus are p53 and Notch1, both of which are also recurrently mutated in cancers of these tissues. From observations taken in human and mouse epithelia, we find that clones carrying p53 and Notch pathway mutations have different clone dynamics which can be explained by their different responses to local cell crowding. p53 mutant clone growth in mouse epidermis approximates a logistic curve, but feedbacks responding to local crowding are required to maintain tissue homeostasis. We go on to show that the observed ability of Notch pathway mutant cells to displace the wild-type population in the mouse oesophageal epithelium reflects a local density feedback that affects both mutant and wild-type cells equally. We then show how these distinct feedbacks are consistent with the distribution of mutations observed in human datasets and are suggestive of a putative mechanism to constrain these cancer-associated mutants.
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Affiliation(s)
- Vasiliki Kostiou
- Department of medical physics and biomedical engineering, UCL, Gower Street, London WC1E 6BT, UK
| | - Michael W. J. Hall
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Philip H. Jones
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Benjamin A. Hall
- Department of medical physics and biomedical engineering, UCL, Gower Street, London WC1E 6BT, UK
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16
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Singleton DA, Pinchbeck GL, Radford AD, Arsevska E, Dawson S, Jones PH, Noble PJM, Williams NJ, Sánchez-Vizcaíno F. Factors Associated with Prescription of Antimicrobial Drugs for Dogs and Cats, United Kingdom, 2014-2016. Emerg Infect Dis 2021; 26:1778-1791. [PMID: 32687030 PMCID: PMC7392421 DOI: 10.3201/eid2608.191786] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Antimicrobial stewardship is a cornerstone of efforts to curtail antimicrobial resistance. To determine factors potentially influencing likelihood of prescribing antimicrobials for animals, we analyzed electronic health records for unwell dogs (n = 155,732 unique dogs, 281,543 consultations) and cats (n = 69,236 unique cats, 111,139 consultations) voluntarily contributed by 173 UK veterinary practices. Using multivariable mixed effects logistic regression, we found that factors associated with decreased odds of systemic antimicrobial prescription were client decisions focused on preventive health: vaccination (dogs, odds ratio [OR] 0.93, 95% CI, 0.90–0.95; cats, OR 0.92, 95% CI 0.89–0.95), insurance (dogs, OR 0.87, 95% CI 0.84–0.90; cats, OR 0.82, 95% CI 0.79–0.86), neutering of dogs (OR 0.90, 95% CI 0.88–0.92), and practices accredited by the Royal College of Veterinary Surgeons (OR 0.79, 95% 95% CI 0.68–0.92). This large multicenter companion animal study demonstrates the potential of preventive healthcare and client engagement to encourage responsible antimicrobial drug use.
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17
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Kostiou V, Zhang H, Hall MWJ, Jones PH, Hall BA. Methods for analysing lineage tracing datasets. R Soc Open Sci 2021; 8:202231. [PMID: 34035949 PMCID: PMC8097194 DOI: 10.1098/rsos.202231] [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] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
A single population of progenitor cells maintains many epithelial tissues. Transgenic mouse cell tracking has frequently been used to study the growth dynamics of competing clones in these tissues. A mathematical model (the 'single-progenitor model') has been argued to reproduce the observed progenitor dynamics accurately. This requires three parameters to describe the growth dynamics observed in transgenic mouse cell tracking-a division rate, a stratification rate and the probability of dividing symmetrically. Deriving these parameters is a time intensive and complex process. We compare the alternative strategies for analysing this source of experimental data, identifying an approximate Bayesian computation-based approach as the best in terms of efficiency and appropriate error estimation. We support our findings by explicitly modelling biological variation and consider the impact of different sampling regimes. All tested solutions are made available to allow new datasets to be analysed following our workflows. Based on our findings, we make recommendations for future experimental design.
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Affiliation(s)
- Vasiliki Kostiou
- Department of Medical Physics and Biomedical Engineering, UCL, Gower Street, London WC1E 6BT, UK
| | - Huairen Zhang
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Michael W. J. Hall
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Philip H. Jones
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Benjamin A. Hall
- Department of Medical Physics and Biomedical Engineering, UCL, Gower Street, London WC1E 6BT, UK
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18
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Collins M, Singleton DA, Noble PJM, Pinchbeck GL, Smith S, Brant B, Smyth S, Radford AD, Appleton C, Jewell C, Rowlingson B, Caddy S, Jones PH. Small animal disease surveillance 2020/21: SARS-CoV-2, syndromic surveillance and an outbreak of acute vomiting in UK dogs. Vet Rec 2021; 188:304. [PMID: 33891730 PMCID: PMC8250639 DOI: 10.1002/vetr.427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Marisol Collins
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - David A Singleton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Peter J M Noble
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Gina L Pinchbeck
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Shirley Smith
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Bethaney Brant
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Steven Smyth
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Alan D Radford
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Charlotte Appleton
- Lancaster Medical School, Lancaster University, Furness Building, Lancaster, LA1 4YG, UK
| | - Christopher Jewell
- Lancaster Medical School, Lancaster University, Furness Building, Lancaster, LA1 4YG, UK
| | - Barry Rowlingson
- Lancaster Medical School, Lancaster University, Furness Building, Lancaster, LA1 4YG, UK
| | - Sarah Caddy
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Trumpington, Cambridge, CB2 0QH, UK
| | - Philip H Jones
- Surveillance Intelligence Unit, APHA, Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
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19
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Fowler JC, King C, Bryant C, Hall MWJ, Sood R, Ong SH, Earp E, Fernandez-Antoran D, Koeppel J, Dentro SC, Shorthouse D, Durrani A, Fife K, Rytina E, Milne D, Roshan A, Mahububani K, Saeb-Parsy K, Hall BA, Gerstung M, Jones PH. Selection of Oncogenic Mutant Clones in Normal Human Skin Varies with Body Site. Cancer Discov 2021; 11:340-361. [PMID: 33087317 PMCID: PMC7116717 DOI: 10.1158/2159-8290.cd-20-1092] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [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: 07/23/2020] [Revised: 09/24/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
Skin cancer risk varies substantially across the body, yet how this relates to the mutations found in normal skin is unknown. Here we mapped mutant clones in skin from high- and low-risk sites. The density of mutations varied by location. The prevalence of NOTCH1 and FAT1 mutations in forearm, trunk, and leg skin was similar to that in keratinocyte cancers. Most mutations were caused by ultraviolet light, but mutational signature analysis suggested differences in DNA-repair processes between sites. Eleven mutant genes were under positive selection, with TP53 preferentially selected in the head and FAT1 in the leg. Fine-scale mapping revealed 10% of clones had copy-number alterations. Analysis of hair follicles showed mutations in the upper follicle resembled adjacent skin, but the lower follicle was sparsely mutated. Normal skin is a dense patchwork of mutant clones arising from competitive selection that varies by location. SIGNIFICANCE: Mapping mutant clones across the body reveals normal skin is a dense patchwork of mutant cells. The variation in cancer risk between sites substantially exceeds that in mutant clone density. More generally, mutant genes cannot be assigned as cancer drivers until their prevalence in normal tissue is known.See related commentary by De Dominici and DeGregori, p. 227.This article is highlighted in the In This Issue feature, p. 211.
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Affiliation(s)
| | | | | | - Michael W J Hall
- Wellcome Sanger Institute, Hinxton, United Kingdom
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Roshan Sood
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Eleanor Earp
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | - Stefan C Dentro
- Wellcome Sanger Institute, Hinxton, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - David Shorthouse
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Amer Durrani
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Kate Fife
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Edward Rytina
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Doreen Milne
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Amit Roshan
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Krishnaa Mahububani
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, Cambridge, United Kingdom
| | - Kourosh Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, Cambridge, United Kingdom
| | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, United Kingdom.
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
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20
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Reynolds G, Vegh P, Fletcher J, Poyner EFM, Stephenson E, Goh I, Botting RA, Huang N, Olabi B, Dubois A, Dixon D, Green K, Maunder D, Engelbert J, Efremova M, Polański K, Jardine L, Jones C, Ness T, Horsfall D, McGrath J, Carey C, Popescu DM, Webb S, Wang XN, Sayer B, Park JE, Negri VA, Belokhvostova D, Lynch MD, McDonald D, Filby A, Hagai T, Meyer KB, Husain A, Coxhead J, Vento-Tormo R, Behjati S, Lisgo S, Villani AC, Bacardit J, Jones PH, O'Toole EA, Ogg GS, Rajan N, Reynolds NJ, Teichmann SA, Watt FM, Haniffa M. Developmental cell programs are co-opted in inflammatory skin disease. Science 2021; 371:eaba6500. [PMID: 33479125 PMCID: PMC7611557 DOI: 10.1126/science.aba6500] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [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: 12/21/2019] [Revised: 09/03/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022]
Abstract
The skin confers biophysical and immunological protection through a complex cellular network established early in embryonic development. We profiled the transcriptomes of more than 500,000 single cells from developing human fetal skin, healthy adult skin, and adult skin with atopic dermatitis and psoriasis. We leveraged these datasets to compare cell states across development, homeostasis, and disease. Our analysis revealed an enrichment of innate immune cells in skin during the first trimester and clonal expansion of disease-associated lymphocytes in atopic dermatitis and psoriasis. We uncovered and validated in situ a reemergence of prenatal vascular endothelial cell and macrophage cellular programs in atopic dermatitis and psoriasis lesional skin. These data illustrate the dynamism of cutaneous immunity and provide opportunities for targeting pathological developmental programs in inflammatory skin diseases.
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Affiliation(s)
- Gary Reynolds
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Peter Vegh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - James Fletcher
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Elizabeth F M Poyner
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Issac Goh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Bayanne Olabi
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology, NHS Lothian, Lauriston Building, Edinburgh EH3 9EN, UK
| | - Anna Dubois
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - David Dixon
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kile Green
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Daniel Maunder
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Mirjana Efremova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Krzysztof Polański
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Claire Jones
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Thomas Ness
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dave Horsfall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Jim McGrath
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Christopher Carey
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dorin-Mirel Popescu
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Simone Webb
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Xiao-Nong Wang
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ben Sayer
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Victor A Negri
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital Campus, London SE1 9RT, UK
| | - Daria Belokhvostova
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital Campus, London SE1 9RT, UK
| | - Magnus D Lynch
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital Campus, London SE1 9RT, UK
| | - David McDonald
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Andrew Filby
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Akhtar Husain
- Department of Pathology, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
| | - Jonathan Coxhead
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0SP, UK
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alexandra-Chloé Villani
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Jaume Bacardit
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, UK
| | - Philip H Jones
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Edel A O'Toole
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Queen Mary University of London, London, UK
| | - Graham S Ogg
- MRC Human Immunology Unit, Oxford Biomedical Research Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Neil Rajan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Nick J Reynolds
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital Campus, London SE1 9RT, UK.
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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21
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De Belly H, Stubb A, Yanagida A, Labouesse C, Jones PH, Paluch EK, Chalut KJ. Membrane Tension Gates ERK-Mediated Regulation of Pluripotent Cell Fate. Cell Stem Cell 2020; 28:273-284.e6. [PMID: 33217323 PMCID: PMC7875115 DOI: 10.1016/j.stem.2020.10.018] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 09/18/2020] [Accepted: 10/28/2020] [Indexed: 12/22/2022]
Abstract
Cell fate transitions are frequently accompanied by changes in cell shape and mechanics. However, how cellular mechanics affects the instructive signaling pathways controlling cell fate is poorly understood. To probe the interplay between shape, mechanics, and fate, we use mouse embryonic stem cells (ESCs), which change shape as they undergo early differentiation. We find that shape change is regulated by a β-catenin-mediated decrease in RhoA activity and subsequent decrease in the plasma membrane tension. Strikingly, preventing a decrease in membrane tension results in early differentiation defects in ESCs and gastruloids. Decreased membrane tension facilitates the endocytosis of FGF signaling components, which activate ERK signaling and direct the exit from the ESC state. Increasing Rab5a-facilitated endocytosis rescues defective early differentiation. Thus, we show that a mechanically triggered increase in endocytosis regulates early differentiation. Our findings are of fundamental importance for understanding how cell mechanics regulates biochemical signaling and therefore cell fate.
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Affiliation(s)
- Henry De Belly
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK; Wellcome/MRC Cambridge Stem Cell Research Institute, Puddicombe Way, University of Cambridge, Cambridge CB2 0AW, UK; Department of Physiology, Development, and Neuroscience, Downing Street, University of Cambridge, Cambridge CB2 3DY, UK
| | - Aki Stubb
- Department of Physiology, Development, and Neuroscience, Downing Street, University of Cambridge, Cambridge CB2 3DY, UK
| | - Ayaka Yanagida
- Wellcome/MRC Cambridge Stem Cell Research Institute, Puddicombe Way, University of Cambridge, Cambridge CB2 0AW, UK; Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Céline Labouesse
- Wellcome/MRC Cambridge Stem Cell Research Institute, Puddicombe Way, University of Cambridge, Cambridge CB2 0AW, UK
| | - Philip H Jones
- Department of Physics & Astronomy, University College London, Gower Street, London WC1E 6BT, UK
| | - Ewa K Paluch
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK; Department of Physiology, Development, and Neuroscience, Downing Street, University of Cambridge, Cambridge CB2 3DY, UK.
| | - Kevin J Chalut
- Wellcome/MRC Cambridge Stem Cell Research Institute, Puddicombe Way, University of Cambridge, Cambridge CB2 0AW, UK.
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22
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Colom B, Alcolea MP, Piedrafita G, Hall MWJ, Wabik A, Dentro SC, Fowler JC, Herms A, King C, Ong SH, Sood RK, Gerstung M, Martincorena I, Hall BA, Jones PH. Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium. Nat Genet 2020; 52:604-614. [PMID: 32424351 PMCID: PMC7116672 DOI: 10.1038/s41588-020-0624-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [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: 10/21/2019] [Accepted: 04/07/2020] [Indexed: 12/29/2022]
Abstract
During aging, progenitor cells acquire mutations, which may generate clones that colonize the surrounding tissue. By middle age, normal human tissues, including the esophageal epithelium (EE), become a patchwork of mutant clones. Despite their relevance for understanding aging and cancer, the processes that underpin mutational selection in normal tissues remain poorly understood. Here, we investigated this issue in the esophageal epithelium of mutagen-treated mice. Deep sequencing identified numerous mutant clones with multiple genes under positive selection, including Notch1, Notch2 and Trp53, which are also selected in human esophageal epithelium. Transgenic lineage tracing revealed strong clonal competition that evolved over time. Clone dynamics were consistent with a simple model in which the proliferative advantage conferred by positively selected mutations depends on the nature of the neighboring cells. When clones with similar competitive fitness collide, mutant cell fate reverts towards homeostasis, a constraint that explains how selection operates in normal-appearing epithelium.
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Affiliation(s)
| | - Maria P Alcolea
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Gabriel Piedrafita
- Wellcome Sanger Institute, Hinxton, UK
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Michael W J Hall
- Wellcome Sanger Institute, Hinxton, UK
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Stefan C Dentro
- Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | | | | | | | | | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | - Benjamin A Hall
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, UK.
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
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23
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Piedrafita G, Kostiou V, Wabik A, Colom B, Fernandez-Antoran D, Herms A, Murai K, Hall BA, Jones PH. A single-progenitor model as the unifying paradigm of epidermal and esophageal epithelial maintenance in mice. Nat Commun 2020; 11:1429. [PMID: 32188860 PMCID: PMC7080751 DOI: 10.1038/s41467-020-15258-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [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: 07/29/2019] [Accepted: 02/26/2020] [Indexed: 01/04/2023] Open
Abstract
In adult skin epidermis and the epithelium lining the esophagus cells are constantly shed from the tissue surface and replaced by cell division. Tracking genetically labelled cells in transgenic mice has given insight into cell behavior, but conflicting models appear consistent with the results. Here, we use an additional transgenic assay to follow cell division in mouse esophagus and the epidermis at multiple body sites. We find that proliferating cells divide at a similar rate, and place bounds on the distribution cell cycle times. By including these results in a common analytic approach, we show that data from eight lineage tracing experiments is consistent with tissue maintenance by a single population of proliferating cells. The outcome of a given cell division is unpredictable but, on average, the likelihood of producing proliferating and differentiating cells is equal, ensuring cellular homeostasis. These findings are key to understanding squamous epithelial homeostasis and carcinogenesis.
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Affiliation(s)
- Gabriel Piedrafita
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro 3, Madrid, 29029, Spain
| | - Vasiliki Kostiou
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | | | | | | | - Albert Herms
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kasumi Murai
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Benjamin A Hall
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
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24
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Hall MW, Shorthouse D, Jones PH, Hall BA. Darwinian Shift: A General Approach for Establishing Evidence and Mechanism of Natural Selection. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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25
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Zendri F, Maciuca IE, Moon S, Jones PH, Wattret A, Jenkins R, Baxter A, Timofte D. Occurrence of ESBL-Producing Escherichia coli ST131, Including the H30-Rx and C1-M27 Subclones, Among Urban Seagulls from the United Kingdom. Microb Drug Resist 2019; 26:697-708. [PMID: 32519936 DOI: 10.1089/mdr.2019.0351] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antimicrobial resistance is a public health concern. Understanding any role that urban seagulls may have as a reservoir of resistant bacteria could be important for reducing transmission. This study investigated fecal Escherichia coli isolates from seagulls (herring gulls and lesser black-backed gulls) to determine the prevalence of extended-spectrum cephalosporin-resistant (ESC-R) and fluoroquinolone-resistant E. coli among gull species from two cities (Taunton and Birmingham) in the United Kingdom (UK). We characterized the genetic background and carriage of plasmid-mediated resistance genes in extended-spectrum β-lactamase (ESBL)-producing E. coli obtained from these birds. Sixty ESC-R E. coli isolates were obtained from 39 seagulls (39/78, 50%), of which 28 (28/60, 46.7%) were positive for plasmid-mediated CTX-M and/or AmpC β-lactamase resistance genes. Among these, blaCTX-M-15, blaCTX-M-14, and blaCMY-2 predominated. Three isolates belonging to the B2-ST131 clone were detected, of which two harbored blaCTX-M-15 (typed to C2/H30Rx) and one harbored blaCTX-M-27 and was typed to C1/H30-R (recently described as the C1-M27 sublineage). The plasmid-mediated quinolone resistance (PMQR) gene carriage prevalence (11.7%) consisted of aac(6')-Ib-cr and qnrB genes. No carbapenem or colistin resistance genes were detected. Urban seagulls in the UK are colonized and can spread major antimicrobial-resistant E. coli isolates harboring ESBL and PMQR determinants, including clinically important strains such as the pandemic clone B2-ST131 and the C1-M27 subclade. This is the first report of ST131-C1-M27 subclade in wildlife in the UK and in seagulls worldwide.
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Affiliation(s)
- Flavia Zendri
- Department of Veterinary Pathology and Public Health, Faculty of Health and Life Sciences, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Iuliana E Maciuca
- Department of Veterinary Pathology and Public Health, Faculty of Health and Life Sciences, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Simon Moon
- Somerset West and Taunton Council, Environmental Health, Taunton, United Kingdom
| | - Philip H Jones
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Neston, United Kingdom
| | - Andy Wattret
- Department of Veterinary Pathology and Public Health, Faculty of Health and Life Sciences, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Richard Jenkins
- School of Allied Health Sciences, De Montfort University, Leicester, United Kingdom
| | - Andy Baxter
- Birdstrike Management Ltd., York, United Kingdom
| | - Dorina Timofte
- Department of Veterinary Pathology and Public Health, Faculty of Health and Life Sciences, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
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26
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Gordon GSD, Joseph J, Alcolea MP, Sawyer T, Williams C, Fitzpatrick CRM, Jones PH, di Pietro M, Fitzgerald RC, Wilkinson TD, Bohndiek SE. Quantitative phase and polarization imaging through an optical fiber applied to detection of early esophageal tumorigenesis. J Biomed Opt 2019; 24:1-13. [PMID: 31840442 PMCID: PMC7006047 DOI: 10.1117/1.jbo.24.12.126004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/18/2019] [Indexed: 05/30/2023]
Abstract
Phase and polarization of coherent light are highly perturbed by interaction with microstructural changes in premalignant tissue, holding promise for label-free detection of early tumors in endoscopically accessible tissues such as the gastrointestinal tract. Flexible optical multicore fiber (MCF) bundles used in conventional diagnostic endoscopy and endomicroscopy scramble phase and polarization, restricting clinicians instead to low-contrast amplitude-only imaging. We apply a transmission matrix characterization approach to produce full-field en-face images of amplitude, quantitative phase, and resolved polarimetric properties through an MCF. We first demonstrate imaging and quantification of biologically relevant amounts of optical scattering and birefringence in tissue-mimicking phantoms. We present an entropy metric that enables imaging of phase heterogeneity, indicative of disordered tissue microstructure associated with early tumors. Finally, we demonstrate that the spatial distribution of phase and polarization information enables label-free visualization of early tumors in esophageal mouse tissues, which are not identifiable using conventional amplitude-only information.
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Affiliation(s)
- George S. D. Gordon
- University of Cambridge, Department of Engineering, Cambridge, United Kingdom
| | - James Joseph
- University of Cambridge, Department of Physics, Cavendish Laboratory, Cambridge, United Kingdom
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Maria P. Alcolea
- University of Cambridge, Wellcome Trust MRC Stem Cell Institute, Cambridge, United Kingdom
| | - Travis Sawyer
- University of Cambridge, Department of Physics, Cavendish Laboratory, Cambridge, United Kingdom
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Calum Williams
- University of Cambridge, Department of Engineering, Cambridge, United Kingdom
- University of Cambridge, Department of Physics, Cavendish Laboratory, Cambridge, United Kingdom
| | | | - Philip H. Jones
- University of Cambridge, MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Massimiliano di Pietro
- University of Cambridge, MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Rebecca C. Fitzgerald
- University of Cambridge, MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | | | - Sarah E. Bohndiek
- University of Cambridge, Department of Physics, Cavendish Laboratory, Cambridge, United Kingdom
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
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27
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Jones PH, Deng B, Winkler J, Zirnheld AL, Ehringer S, Shetty V, Cox M, Nguyen H, Shen WJ, Huang TT, Wang E. Over-expression of miR-34c leads to early-life visceral fat accumulation and insulin resistance. Sci Rep 2019; 9:13844. [PMID: 31554925 PMCID: PMC6761099 DOI: 10.1038/s41598-019-50191-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Overweight children and adolescents are at high risk for adult and late life obesity. This report investigates some underlying mechanisms contributing to obesity during early life in an animal model. We generated a strain of transgenic mice, cU2, overexpressing human microRNA 34c, a microRNA functionally implicated in adipogenesis. Male and female cU2 mice exhibit significant weight gain, accompanied by marked increase in abdominal fat mass and metabolic abnormalities, including reduction of both glucose clearance rate and insulin sensitivity, as early as two months of age. Adipogenesis derailment at this early age is suggested by decreased expression of adiponectin, the fat mass and obesity-associated gene, and the adiponectin receptor R1, coupled with a reduction of the brown fat biomarker PAT2 and the adipogenesis inhibitor SIRT1. Notably, adiponectin is an important adipokine and an essential regulator of glucose and fatty acid homeostasis. cU2 mice may provide a crucial animal model for investigating the role of miR-34c in early onset insulin resistance and visceral fat mass increase, contributing to accelerated body weight gain and metabolic disorders. Intervention in this dysregulation may open a new preventive strategy to control early-life weight gain and abnormal insulin resistance, and thus prevalent adult and late life obesity.
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Affiliation(s)
| | - Brian Deng
- Palo Alto Veterans Institute for Research, Palo Alto, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | | | - Matthew Cox
- Advanced Genomic Technology, LLC, Louisville, KY, USA
| | - Huy Nguyen
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Wen-Jun Shen
- Department of Endocrinology, Stanford University School of Medicine, Stanford, CA, USA.,Geriatric Research, Education, and Clinical Center, VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Ting-Ting Huang
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA. .,Geriatric Research, Education, and Clinical Center, VA Palo Alto Health Care System, Palo Alto, CA, USA.
| | - Eugenia Wang
- Advanced Genomic Technology, LLC, Louisville, KY, USA
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28
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Fernandez-Antoran D, Piedrafita G, Murai K, Ong SH, Herms A, Frezza C, Jones PH. Outcompeting p53-Mutant Cells in the Normal Esophagus by Redox Manipulation. Cell Stem Cell 2019; 25:329-341.e6. [PMID: 31327664 PMCID: PMC6739485 DOI: 10.1016/j.stem.2019.06.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/14/2019] [Accepted: 06/14/2019] [Indexed: 12/20/2022]
Abstract
As humans age, normal tissues, such as the esophageal epithelium, become a patchwork of mutant clones. Some mutations are under positive selection, conferring a competitive advantage over wild-type cells. We speculated that altering the selective pressure on mutant cell populations may cause them to expand or contract. We tested this hypothesis by examining the effect of oxidative stress from low-dose ionizing radiation (LDIR) on wild-type and p53 mutant cells in the transgenic mouse esophagus. We found that LDIR drives wild-type cells to stop proliferating and differentiate. p53 mutant cells are insensitive to LDIR and outcompete wild-type cells following exposure. Remarkably, combining antioxidant treatment and LDIR reverses this effect, promoting wild-type cell proliferation and p53 mutant differentiation, reducing the p53 mutant population. Thus, p53-mutant cells can be depleted from the normal esophagus by redox manipulation, showing that external interventions may be used to alter the mutational landscape of an aging tissue.
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Affiliation(s)
| | | | - Kasumi Murai
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Albert Herms
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Box 196, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; MRC Cancer Unit, University of Cambridge, Box 196, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK.
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29
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Abstract
Cancer develops from mutated cells in normal tissues. Whether somatic mutations alter normal cell dynamics is key to understanding cancer risk and guiding interventions to reduce it. An analysis of the first incomplete moment of size distributions of clones carrying cancer-associated mutations in normal human eyelid skin gives a good fit with neutral drift, arguing mutations do not affect cell fate. However, this suggestion conflicts with genetic evidence in the same dataset that argues for strong positive selection of a subset of mutations. This implies cells carrying these mutations have a competitive advantage over normal cells, leading to large clonal expansions within the tissue. In the normal epithelium, clone growth is constrained by the limited size of the proliferating compartment and competition with surrounding cells. We show that if these factors are taken into account, the first incomplete moment of the clone size distribution is unable to exclude non-neutral behaviour. Furthermore, experimental factors can make a non-neutral clone size distribution appear neutral. We validate these principles with a new experimental dataset showing that when experiments are appropriately designed, the first incomplete moment can be a useful indicator of non-neutral competition. Finally, we discuss the complex relationship between mutant clone sizes and genetic selection.
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Affiliation(s)
- Michael W. J. Hall
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Philip H. Jones
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Benjamin A. Hall
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
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30
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Singleton DA, Noble PJM, Sánchez-Vizcaíno F, Dawson S, Pinchbeck GL, Williams NJ, Radford AD, Jones PH. Pharmaceutical Prescription in Canine Acute Diarrhoea: A Longitudinal Electronic Health Record Analysis of First Opinion Veterinary Practices. Front Vet Sci 2019; 6:218. [PMID: 31334254 PMCID: PMC6615257 DOI: 10.3389/fvets.2019.00218] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/18/2019] [Indexed: 12/17/2022] Open
Abstract
Canine acute diarrhoea is frequently observed in first opinion practice, though little is known about commonly used diagnostic or therapeutic management plans, including use of antimicrobials. This retrospective observational study utilised electronic health records augmented with practitioner-completed questionnaires from 3,189 cases (3,159 dogs) collected from 179 volunteer veterinary practices between April 2014 and January 2017. We used multivariable analysis to explore factors potentially associated with pharmaceutical agent prescription, and resolution of clinical signs by 10 days post-initial presentation. Use of bacteriological and/or parasitological diagnostic tests were uncommon (3.2% of cases, 95% confidence interval, CI, 2.4–4.0), though systemic antimicrobials were the most commonly prescribed pharmaceutical agents (49.7% of cases, 95% CI 46.1–53.2). Such prescription was associated with haemorrhagic diarrhoea (odds ratio, OR, 4.1; 95% CI 3.4–5.0), body temperature in excess of 39.0°C, or moderate/severe cases (OR 1.3, 95% CI 1.1–1.7). Gastrointestinal agents (e.g., antacids) were prescribed to 37.7% of cases (95% CI 35.4–39.9), and were most frequently prescribed to vomiting dogs regardless of presence (OR 46.4, 95% CI 19.4–110.8) or absence of blood (OR 17.1, 95% CI 13.4–21.9). Endoparasiticides/endectocides were prescribed to 7.8% of cases (95% CI 6.8–9.0), such prescription being less frequent for moderate/severe cases (OR 0.5, 95% CI 0.4–0.7), though more frequent when weight loss was recorded (OR 3.4, 95% CI 1.3–9.0). Gastrointestinal nutraceuticals (e.g., probiotics) were dispensed to 60.8% of cases (95% CI 57.1–64.6), these cases less frequently presenting with moderate/severe clinical signs (OR 0.6, 95% CI 0.5–0.8). Nearly a quarter of cases were judged lost to follow-up (n=754). Insured (OR 0.7, 95% CI 0.5–0.9); neutered (OR 0.4, 95% CI 0.3–0.5), or vaccinated dogs (OR 0.3, 95% CI 0.3–0.4) were less commonly lost to follow-up. Of remaining dogs, clinical signs were deemed resolved in 95.4% of cases (95% CI 94.6–96.2). Provision of dietary modification advice and gastrointestinal nutraceuticals alone were positively associated with resolution (OR 2.8, 95% CI 1.3–6.1); no such associations were found for pharmaceutical agents, including antimicrobials. Hence, this study supports the view that antimicrobials are largely unnecessary for acute diarrhoea cases; this being of particular importance when considering the global threat posed by antimicrobial resistance.
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Affiliation(s)
- David A Singleton
- Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Neston, United Kingdom
| | - P J M Noble
- Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | | | - Susan Dawson
- Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Gina L Pinchbeck
- Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Neston, United Kingdom
| | - Nicola J Williams
- Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Neston, United Kingdom
| | - Alan D Radford
- Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Neston, United Kingdom
| | - Philip H Jones
- Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Neston, United Kingdom
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31
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Singleton DA, Arsevska E, Smyth S, Barker EN, Jewell C, Brant B, Sánchez-Vizcaíno F, Dawson S, Pinchbeck GL, Noble PJ, Jones PH, Radford AD. Small animal disease surveillance: gastrointestinal disease, antibacterial prescription and Tritrichomonas foetus. Vet Rec 2019; 184:211-216. [DOI: 10.1136/vr.l722] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | | | | | | | - Christopher Jewell
- Lancaster Medical School, Lancaster University; Furness Building Lancaster LA1 4YG UK
| | | | | | - Susan Dawson
- Institute of Veterinary Science, University of Liverpool; Leahurst Campus, Neston CH64 7TE UK
| | | | - Peter J.M. Noble
- Institute of Veterinary Science, University of Liverpool; Leahurst Campus, Neston CH64 7TE UK
| | - Philip H. Jones
- Surveillance Intelligence Unit; Animal and Plant Health Agency; Kendal Road, Harlescott, Shrewsbury SY1 4HD UK
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32
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Leiter LA, Tinahones FJ, Karalis DG, Bujas-Bobanovic M, Letierce A, Mandel J, Samuel R, Jones PH. Alirocumab safety in people with and without diabetes mellitus: pooled data from 14 ODYSSEY trials. Diabet Med 2018; 35:1742-1751. [PMID: 30183102 PMCID: PMC6585811 DOI: 10.1111/dme.13817] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/03/2018] [Indexed: 02/06/2023]
Abstract
AIM To evaluate the safety of the proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitor alirocumab according to diabetes mellitus status. METHODS Safety data from 14 trials (8-104-week durations) were analysed by treatment (alirocumab or placebo/ezetimibe control) and diabetes status (yes/no, defined by medical history). Adverse event data were assessed using descriptive statistics and Cox models. RESULTS Of the 5234 trial participants, 1554 (29.7%) had diabetes. Overall, treatment-emergent adverse events were similar in the alirocumab and control groups, except for more frequent local injection site reactions with alirocumab. Fewer people with diabetes experienced local injection site reactions [alirocumab, 3.5%, control, 2.9%; hazard ratio 1.24 (95% CI 0.68-2.25)] than those without diabetes [alirocumab, 7.5%; control, 4.9%; hazard ratio 1.51 (95% CI 1.13-2.01)]. Those with diabetes reported a greater number of serious adverse events (alirocumab, 19.4%; control, 19.7%) than those without diabetes (alirocumab, 14.5%; control, 13.5%). In people with diabetes, major adverse cardiac events occurred in 2.7% of alirocumab-treated people [control, 3.3%; hazard ratio 0.74 (95% CI 0.41-1.35)]; in those without diabetes, 1.8% of alirocumab-treated people had major adverse cardiac events [control, 1.7%; hazard ratio 0.95 (95% CI 0.56-1.62)]. Overall, no increase in HbA1c or fasting plasma glucose vs control treatment groups was observed, regardless of diabetes status. CONCLUSION This pooled analysis across 14 trials demonstrated similar safety for alirocumab vs control treatment, irrespective of diabetes status, except for more frequent local injection site reactions with alirocumab. People with diabetes reported fewer local injection site reactions than those without diabetes.
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Affiliation(s)
- L A Leiter
- Li Ka Shing Knowledge Institute, St Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - F J Tinahones
- Department of Clinical Endocrinology and Nutrition (IBIMA), Hospital Virgen de la Victoria, University of Málaga, CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Málaga, Spain
| | - D G Karalis
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - A Letierce
- Biostatistics and Programming Department, Sanofi, Chilly-Mazarin, France
| | - J Mandel
- IviData Stats, Levallois Perret, France
- Sanofi, Chilly-Mazarin, France
| | - R Samuel
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - P H Jones
- Baylor College of Medicine, Houston, TX, USA
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Martincorena I, Fowler JC, Wabik A, Lawson ARJ, Abascal F, Hall MWJ, Cagan A, Murai K, Mahbubani K, Stratton MR, Fitzgerald RC, Handford PA, Campbell PJ, Saeb-Parsy K, Jones PH. Somatic mutant clones colonize the human esophagus with age. Science 2018; 362:911-917. [PMID: 30337457 PMCID: PMC6298579 DOI: 10.1126/science.aau3879] [Citation(s) in RCA: 619] [Impact Index Per Article: 103.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/03/2018] [Indexed: 12/16/2022]
Abstract
The extent to which cells in normal tissues accumulate mutations throughout life is poorly understood. Some mutant cells expand into clones that can be detected by genome sequencing. We mapped mutant clones in normal esophageal epithelium from nine donors (age range, 20 to 75 years). Somatic mutations accumulated with age and were caused mainly by intrinsic mutational processes. We found strong positive selection of clones carrying mutations in 14 cancer genes, with tens to hundreds of clones per square centimeter. In middle-aged and elderly donors, clones with cancer-associated mutations covered much of the epithelium, with NOTCH1 and TP53 mutations affecting 12 to 80% and 2 to 37% of cells, respectively. Unexpectedly, the prevalence of NOTCH1 mutations in normal esophagus was several times higher than in esophageal cancers. These findings have implications for our understanding of cancer and aging.
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Affiliation(s)
| | - Joanna C Fowler
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Agnieszka Wabik
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | | | - Michael W J Hall
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Kasumi Murai
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Krishnaa Mahbubani
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge CB2 2QQ, UK
| | | | - Rebecca C Fitzgerald
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Penny A Handford
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge CB2 2QQ, UK
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.
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Singleton DA, Sánchez-Vizcaíno F, Arsevska E, Dawson S, Jones PH, Noble PJM, Pinchbeck GL, Williams NJ, Radford AD. New approaches to pharmacosurveillance for monitoring prescription frequency, diversity, and co-prescription in a large sentinel network of companion animal veterinary practices in the United Kingdom, 2014-2016. Prev Vet Med 2018; 159:153-161. [PMID: 30314778 PMCID: PMC6193134 DOI: 10.1016/j.prevetmed.2018.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/04/2018] [Accepted: 09/04/2018] [Indexed: 10/28/2022]
Abstract
Pharmaceutical agents (PAs) are commonly prescribed in companion animal practice in the United Kingdom. However, little is known about PA prescription on a population-level, particularly with respect to PAs authorised for human use alone prescribed via the veterinary cascade; this raises important questions regarding the efficacy and safety of PAs prescribed to companion animals. This study explored new approaches for describing PA prescription, diversity and co-prescription in dogs, cats and rabbits utilising electronic health records (EHRs) from a sentinel network of 457 companion animal-treating veterinary sites throughout the UK over a 2-year period (2014-2016). A novel text mining-based identification and classification methodology was utilised to semi-automatically map practitioner-defined product descriptions recorded in 918,333 EHRs from 413,870 dogs encompassing 1,242,270 prescriptions; 352,730 EHRs from 200,541 cats encompassing 491,554 prescriptions, and 22,526 EHRS from 13,398 rabbits encompassing 18,490 prescriptions respectively. PA prescription as a percentage of booked consultations was 65.4% (95% confidence interval, CI, 64.6-66.3) in dogs; in cats it was 69.1% (95% CI, 67.9-70.2) and in rabbits, 56.3% (95% CI, 54.7-57.8). Vaccines were the most commonly prescribed PAs in all three species, with antibiotics, antimycotics, and parasiticides also commonly prescribed. PA prescription utilising products authorised for human use only (hence, 'human-authorised') comprised 5.1% (95% CI, 4.7-5.5) of total canine prescription events; in cats it was 2.8% (95% CI, 2.6-3.0), and in rabbits, 7.8% (95% CI, 6.5-9.0). The most commonly prescribed human-authorised PA in dogs was metronidazole (antibiotic); in cats and rabbits it was ranitidine (H2 histamine receptor antagonist). Using a new approach utilising the Simpson's Diversity Index (an ecological measure of relative animal, plant etc. species abundance), we identified differences in prescription based on presenting complaint and species, with rabbits generally exposed to a less diverse range of PAs than dogs or cats, potentially reflecting the paucity of authorised PAs for use in rabbits. Finally, through a novel application of network analysis, we demonstrated the existence of three major co-prescription groups (preventive health; treatment of disease, and euthanasia); a trend commonly observed in practice. This study represents the first time PA prescription has been described across all pharmaceutical families in a large population of companion animals, encompassing PAs authorised for both veterinary and human-only use. These data form a baseline against which future studies could be compared, and provides some useful tools for understanding PA comparative efficacy and risks when prescribed in the varied setting of clinical practice.
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Affiliation(s)
- D A Singleton
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom.
| | - F Sánchez-Vizcaíno
- National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, The Farr Institute @ HeRC, University of Liverpool, Waterhouse Building, Liverpool, L69 3GL, United Kingdom
| | - E Arsevska
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom
| | - S Dawson
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom
| | - P H Jones
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom
| | - P J M Noble
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom
| | - G L Pinchbeck
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom
| | - N J Williams
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom
| | - A D Radford
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom
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Murai K, Skrupskelyte G, Piedrafita G, Hall M, Kostiou V, Ong SH, Nagy T, Cagan A, Goulding D, Klein AM, Hall BA, Jones PH. Epidermal Tissue Adapts to Restrain Progenitors Carrying Clonal p53 Mutations. Cell Stem Cell 2018; 23:687-699.e8. [PMID: 30269904 PMCID: PMC6224607 DOI: 10.1016/j.stem.2018.08.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/10/2018] [Accepted: 08/28/2018] [Indexed: 12/23/2022]
Abstract
Aging human tissues, such as sun-exposed epidermis, accumulate a high burden of progenitor cells that carry oncogenic mutations. However, most progenitors carrying such mutations colonize and persist in normal tissue without forming tumors. Here, we investigated tissue-level constraints on clonal progenitor behavior by inducing a single-allele p53 mutation (Trp53R245W; p53∗/wt), prevalent in normal human epidermis and squamous cell carcinoma, in transgenic mouse epidermis. p53∗/wt progenitors initially outcompeted wild-type cells due to enhanced proliferation, but subsequently reverted toward normal dynamics and homeostasis. Physiological doses of UV light accelerated short-term expansion of p53∗/wt clones, but their frequency decreased with protracted irradiation, possibly due to displacement by UV-induced mutant clones with higher competitive fitness. These results suggest multiple mechanisms restrain the proliferation of p53∗/wt progenitors, thereby maintaining epidermal integrity.
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Affiliation(s)
| | | | | | - Michael Hall
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Vasiliki Kostiou
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | | | - Tibor Nagy
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin A Hall
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK.
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36
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Arsevska E, Singleton DA, Jewell C, Paterson S, Jones PH, Smyth S, Brant B, Dawson S, Noble PJM, Sánchez-Vizcaíno F, Radford AD. Small animal disease surveillance: pruritus and Pseudomonas skin infections. Vet Rec 2018; 183:182-187. [PMID: 30093432 DOI: 10.1136/vr.k3462] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
| | | | - Christopher Jewell
- Lancaster Medical School, Lancaster University, Furness Building, Lancaster LA1 4YG, UK
| | - Susan Paterson
- Rutland House Referrals, Abbotsfield Road, St Helens WA9 4HU, UK
| | | | | | | | - Susan Dawson
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | - Peter J M Noble
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
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Abstract
Pyotr Kapitza studied in 1951 the unusual equilibrium features of a rigid pendulum when its point of suspension is under a high-frequency vertical vibration. A sufficiently fast vibration makes the top position stable, putting the pendulum in an inverted orientation that seemingly defies gravity. Kapitza’s analytical method, based on an asymptotic separation of fast and slow variables yielding a renormalized potential, has found application in many diverse areas. Here we study Kapitza’s pendulum going beyond its typical idealizations, by explicitly considering its finite stiffness and the dissipative interaction with the surrounding medium, and using similar theoretical methods as Kapitza. The pendulum is realized at the micrometre scale using a colloidal particle suspended in water and trapped by optical tweezers. Though the strong dissipation present at this scale prevents the inverted pendulum regime, new ones appear in which the equilibrium positions are displaced to the side, and with transitions between them determined either by the driving frequency or the friction coefficient. These new regimes could be exploited in applications aimed at particle separation at small scales.
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Affiliation(s)
- Christopher J Richards
- Department of Physics & Astronomy, University College London, Gower Street, London, WC1E 6BT, UK
| | - Thomas J Smart
- Department of Physics & Astronomy, University College London, Gower Street, London, WC1E 6BT, UK
| | - Philip H Jones
- Department of Physics & Astronomy, University College London, Gower Street, London, WC1E 6BT, UK
| | - David Cubero
- Departamento de Fisica Aplicada I, EPS, Universidad de Sevilla, Calle Virgen de África 7, 41011, Sevilla, Spain.
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38
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Agrawal R, Ang B, Balne PK, Richards C, Smart T, Cardoso J, Shima D, Jones PH, Pavesio C. Non-Occlusive Retinal Vascular Inflammation and Role of Red Blood Cell Deformability in Birdshot Chorioretinopathy. Ocul Immunol Inflamm 2018; 27:978-986. [PMID: 29985708 DOI: 10.1080/09273948.2018.1485959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Purpose: To investigate differences in red blood cell (RBC) deformability between birdshot chorioretinopathy (BCR) subjects and matched controls, and to postulate its relationship with lack of vascular occlusion in BCR. Methods: In a single center, prospective, non-randomized mechanistic study, blood samples were collected from eight healthy controls and nine BCR patients, and subjected to biochemical and hematological tests, as well as RBC indices assessment using dual-beam optical tweezers. Results: The mean age of the controls was 52.37 ± 10.70 years and BCR patients was 53.44 ± 12.39 years. Initial cell size (Io) for the controls was 8.48 ± 0.25 μm and 8.87 ± 0.31 μm for BCR RBCs (p = 0.014). The deformability index (DI) for the controls was 0.066 ± 0.02 and that for BCR RBCs was 0.063 ± 0.03 (p = 0.441). Conclusion: There was no statistically significant difference in DI between RBCs from BCR and healthy controls. This may explain the rare occurrence of retinal vascular occlusion despite the underlying vasculitic pathophysiology of BCR.
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Affiliation(s)
- Rupesh Agrawal
- Moorfields Eye Hospital, NHS Foundation Trust , London , UK.,National Healthcare Group Eye Institute, Tan Tock Seng Hospital , Singapore.,Department of Mechanical Engineering, University College London , London , UK.,Institute of Ophthalmology, University College London , London , UK
| | - Bryan Ang
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital , Singapore
| | - Praveen Kumar Balne
- Translational Pre-Clinical Model Platform, Singapore Eye Research Institute , Singapore
| | | | - Thomas Smart
- Department of Physics and Astronomy, University College London , London , UK
| | - João Cardoso
- Moorfields Eye Hospital, NHS Foundation Trust , London , UK
| | - David Shima
- Institute of Ophthalmology, University College London , London , UK
| | - Philip H Jones
- Department of Physics and Astronomy, University College London , London , UK
| | - Carlos Pavesio
- Moorfields Eye Hospital, NHS Foundation Trust , London , UK.,Institute of Ophthalmology, University College London , London , UK
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39
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Turner R, Arsevska E, Brant B, Singleton DA, Newman J, Noble PM, Jones PH, Radford AD. Risk factors for cutaneous myiasis (blowfly strike) in pet rabbits in Great Britain based on text-mining veterinary electronic health records. Prev Vet Med 2018; 153:77-83. [PMID: 29653739 PMCID: PMC5910172 DOI: 10.1016/j.prevetmed.2018.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/01/2018] [Accepted: 03/13/2018] [Indexed: 12/03/2022]
Abstract
Blowfly strike is a devastating and often rapidly fatal disease in rabbits. In Great Britain (GB), Lucilia sericata is the primary causative species. Despite its severity, there has been minimal investigatory work into the disease in rabbits. Here we used text mining to screen electronic health records (EHRs) from a large sentinel network of 389 veterinary practices in GB between March 2014 and April 2017 for confirmed cases of blowfly strike in rabbits. Blowfly strike was identified in 243 of 42,226 rabbit consultations (0.6%), affecting 205 individual rabbits. The anatomical site of recorded blowfly strike lesions was overwhelmingly the perineal area (n = 109, 52.4%). Less commonly lesions were observed affecting other areas of the body (n = 9, 4.3%) and head (n = 8, 3.8%); in 83 consultations (39.9%), the affected area was not specified. Of the rabbits presenting with blowfly strike, 44.7% were recorded as being euthanized or died. A case control study was used to identify risk factors for blowfly strike in this population. Whilst sex and neuter status in isolation were not significantly associated with blowfly strike, entire female rabbits showed a 3.3 times greater odds of being a case than neutered female rabbits. Rabbits five years of age and over were more than 3.8 times likely to present for blowfly strike. For every 1 °C rise in environmental temperature between 4.67 °C and 17.68 °C, there was a 33% increase risk of blowfly strike, with cases peaking in July or August. Overall blowfly strike cases started earlier and peaked higher in the south of Great Britain. The most northerly latitude studied was at lower risk of blowfly strike than the most southerly (OR = 0.50, p < 0.001). There appeared to be no significant relationship between blowfly strike in rabbits and either the sheep density or rural and urban land coverage types. The results presented here can be used for targeted health messaging to reduce the impact of this deadly disease for rabbits. We propose that real-time temporal and spatial surveillance of the rabbit disease may also help inform sheep control, where the seasonal profile is very similar, and where routine surveillance data is also not available. Our results highlight the value of sentinel databases based on EHRs for research and surveillance.
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Affiliation(s)
- Rachel Turner
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, UK
| | - Elena Arsevska
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, UK
| | - Beth Brant
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, UK
| | - David A Singleton
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, UK
| | - Jenny Newman
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, UK
| | - Pj-M Noble
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, UK
| | - Philip H Jones
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, UK
| | - Alan D Radford
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, UK.
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40
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Arsevska E, Priestnall SL, Singleton DA, Jones PH, Smyth S, Brant B, Dawson S, Sánchez-Vizcaíno F, Noble PJM, Radford AD. Small animal disease surveillance: respiratory disease 2017. Vet Rec 2018; 182:369-373. [PMID: 29599257 DOI: 10.1136/vr.k1426] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
| | - Simon L Priestnall
- Department of Pathobiology & Population Sciences, Royal Veterinary College, North Mymms, Hatfield AL9 7TA, UK
| | | | | | | | | | - Susan Dawson
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | | | - Peter J M Noble
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
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42
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Donato MG, Messina E, Foti A, Smart TJ, Jones PH, Iatì MA, Saija R, Gucciardi PG, Maragò OM. Optical trapping and optical force positioning of two-dimensional materials. Nanoscale 2018; 10:1245-1255. [PMID: 29292452 DOI: 10.1039/c7nr06465a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In recent years, considerable effort has been devoted to the synthesis and characterization of two-dimensional materials. Liquid phase exfoliation (LPE) represents a simple, large-scale method to exfoliate layered materials down to mono- and few-layer flakes. In this context, the contactless trapping, characterization, and manipulation of individual nanosheets hold perspectives for increased accuracy in flake metrology and the assembly of novel functional materials. Here, we use optical forces for high-resolution structural characterization and precise mechanical positioning of nanosheets of hexagonal boron nitride, molybdenum disulfide, and tungsten disulfide obtained by LPE. Weakly optically absorbing nanosheets of boron nitride are trapped in optical tweezers. The analysis of the thermal fluctuations allows a direct measurement of optical forces and the mean flake size in a liquid environment. Measured optical trapping constants are compared with T-matrix light scattering calculations to show a quadratic size scaling for small size, as expected for a bidimensional system. In contrast, strongly absorbing nanosheets of molybdenum disulfide and tungsten disulfide are not stably trapped due to the dominance of radiation pressure over the optical trapping force. Thus, optical forces are used to pattern a substrate by selectively depositing nanosheets in short times (minutes) and without any preparation of the surface. This study will be useful for improving ink-jet printing and for a better engineering of optoelectronic devices based on two-dimensional materials.
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Affiliation(s)
- M G Donato
- CNR-IPCF, Istituto per i Processi Chimico-Fisici, V.le F. Stagno D'Alcontres 37, I-98158, Messina, Italy.
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43
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Noble PJM, Newman J, Wyatt AM, Radford AD, Jones PH. Heightened risk of canine chocolate exposure at Christmas and Easter. Vet Rec 2017; 181:684. [PMID: 29263290 PMCID: PMC5749306 DOI: 10.1136/vr.104762] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/05/2017] [Indexed: 11/24/2022]
Affiliation(s)
- Peter-John M Noble
- Small Animal Teaching Hospital, University of Liverpool, Institute of Veterinary Science, Neston, UK
| | - Jenny Newman
- Department of Epidemiology and Population Health, University of Liverpool, Institute of Infection and Global Health, Neston, UK
| | - Alison M Wyatt
- University of Liverpool, Institute of Veterinary Science, Neston, UK
| | - Alan D Radford
- Department of Infection Biology, University of Liverpool, Institute of Infection and Global Health, Neston, UK
| | - Philip H Jones
- Department of Epidemiology and Population Health, University of Liverpool, Institute of Infection and Global Health, Neston, UK
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44
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Arsevska E, Singleton D, Sánchez-Vizcaíno F, Williams N, Jones PH, Smyth S, Heayns B, Wardeh M, Radford AD, Dawson S, Noble PJM, Davies RH. Small animal disease surveillance: GI disease and salmonellosis. Vet Rec 2017; 181:228-232. [PMID: 28864509 DOI: 10.1136/vr.j3642] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Presentation for gastrointestinal (GI) disease comprised 2.2 per cent of cat, 3.2 per cent of dog and 2.2 per cent of rabbit consultations between April 1, 2016 and March 31, 2017Diarrhoea and vomiting without blood were the most frequently reported GI disease clinical signs (34.4 and 38.9 per cent in cats and 42.8 and 37.3 per cent in dogs, respectively)The mean percentage of samples testing positive for Salmonella in dogs was double that in cats (0.82 per cent and 0.41 per cent, respectively) from January 1, 2011 to December 31, 2016In dogs, autumn was associated with a greater proportion of Salmonella-positive sample submissions; no clear suggestion of seasonal variation in cats was observedIn both cats and dogs, isolates belonging to Salmonella enterica group B serotypes were the most common (68.9 per cent in cats and 55.0 per cent in dogs).
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Affiliation(s)
- Elena Arsevska
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK.,* These authors contributed equally
| | - David Singleton
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK.,* These authors contributed equally
| | - Fernando Sánchez-Vizcaíno
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK.,* These authors contributed equally
| | - Nicola Williams
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
| | - Philip H Jones
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
| | - Steven Smyth
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
| | - Bethaney Heayns
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
| | - Maya Wardeh
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
| | - Alan D Radford
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
| | - Susan Dawson
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
| | - Peter J M Noble
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
| | - Robert H Davies
- Bacteriology Department, APHA Weybridge, Addlestone, Surrey KT15 3NB, UK
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45
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Abstract
Multiple scattering of light induces structured interactions, or optical binding forces, between collections of small particles. This has been extensively studied in the case of microspheres. However, binding forces are strongly shape dependent: here, we turn our attention to dielectric nanowires. Using a novel numerical model we uncover rich behavior. The extreme geometry of the nanowires produces a sequence of stationary and dynamic states. In linearly polarized light, thermally stable ladder-like structures emerge. Lower symmetry, sagittate arrangements can also arise, whose configurational asymmetry unbalances the optical forces leading to nonconservative, translational motion. Finally, the addition of circular polarization drives a variety of coordinated rotational states whose dynamics expose fundamental properties of optical spin. These results suggest that optical binding can provide an increased level of control over the positions and motions of nanoparticles, opening new possibilities for driven self-organization and heralding a new field of self-assembling optically driven micromachines.
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Affiliation(s)
- Stephen H Simpson
- Institute of Scientific Instruments of the CAS , Kràlovopolskà 147, 612 64 Brno, Czech Republic
| | - Pavel Zemánek
- Institute of Scientific Instruments of the CAS , Kràlovopolskà 147, 612 64 Brno, Czech Republic
| | - Onofrio M Maragò
- CNR-IPCF, Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche , Viale F. Stagno D'Alcontres 37, I-98158 Messina, Italy
| | - Philip H Jones
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, U.K
| | - Simon Hanna
- H. H. Wills Physics Laboratory, University of Bristol , Tyndall Avenue, Bristol BS8 1TL, U.K
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Singleton DA, Sánchez-Vizcaíno F, Dawson S, Jones PH, Noble PJM, Pinchbeck GL, Williams NJ, Radford AD. Patterns of antimicrobial agent prescription in a sentinel population of canine and feline veterinary practices in the United Kingdom. Vet J 2017; 224:18-24. [PMID: 28697871 PMCID: PMC5518771 DOI: 10.1016/j.tvjl.2017.03.010] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 11/04/2022]
Abstract
Antimicrobial agent prescription was monitored in a large UK population of cats and dogs over a 2 year period (2014–2016). Systemic antimicrobial agents were prescribed more frequently to cats; topical prescription was more frequent in dogs. A temporal reduction (2014–2016) in antimicrobial agent prescription was observed in both cats and dogs in this population. Premises which prescribed antimicrobial agents commonly to cats generally also prescribed commonly to dogs. The most frequently prescribed antibiotics were cefovecin in cats and clavulanic acid potentiated amoxicillin in dogs.
Antimicrobial resistance is an increasingly important global health threat and the use of antimicrobial agents is a key risk factor in its development. This study describes antimicrobial agent prescription (AAP) patterns over a 2 year period using electronic health records (EHRs) from booked consultations in a network of 457 sentinel veterinary premises in the United Kingdom. A semi-automated classification methodology was used to map practitioner defined product codes in 918,333 EHRs from 413,870 dogs and 352,730 EHRs from 200,541 cats, including 289,789 AAPs. AAP as a proportion of total booked consultations was more frequent in dogs (18.8%, 95% confidence interval, CI, 18.2–19.4) than cats (17.5%, 95% CI 16.9–18.1). Prescription of topical antimicrobial agents was more frequent in dogs (7.4%, 95% CI 7.2–7.7) than cats (3.2%, 95% CI 3.1–3.3), whilst prescription of systemic antimicrobial agents was more frequent in cats (14.8%, 95% CI 14.2–15.4) than dogs (12.2%, 95% CI 11.7–12.7). A decreasing temporal pattern was identified for prescription of systemic antimicrobial agents in dogs and cats. Premises which prescribed antimicrobial agents frequently for dogs also prescribed frequently for cats. AAP was most frequent during pruritus consultations in dogs and trauma consultations in cats. Clavulanic acid potentiated amoxicillin was the most frequently prescribed antimicrobial agent in dogs (28.6% of prescriptions, 95% CI 27.4–29.8), whereas cefovecin, a third generation cephalosporin, was the most frequently prescribed antimicrobial agent in cats (36.2%, 95% CI 33.9–38.5). This study demonstrated patterns in AAP over time and for different conditions in a population of companion animals in the United Kingdom.
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Affiliation(s)
- D A Singleton
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom.
| | - F Sánchez-Vizcaíno
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom; National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, The Farr Institute @ HeRC, University of Liverpool, Waterhouse Building, Liverpool, L69 3GL, United Kingdom
| | - S Dawson
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom
| | - P H Jones
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom
| | - P J M Noble
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom
| | - G L Pinchbeck
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom
| | - N J Williams
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom
| | - A D Radford
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, CH64 7TE, United Kingdom
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47
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Memoli G, Fury CR, Baxter KO, Gélat PN, Jones PH. Acoustic force measurements on polymer-coated microbubbles in a microfluidic device. J Acoust Soc Am 2017; 141:3364. [PMID: 28599556 PMCID: PMC5436981 DOI: 10.1121/1.4979933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This work presents an acoustofluidic device for manipulating coated microbubbles, designed for the simultaneous use of optical and acoustical tweezers. A comprehensive characterization of the acoustic pressure in the device is presented, obtained by the synergic use of different techniques in the range of acoustic frequencies where visual observations showed aggregation of polymer-coated microbubbles. In absence of bubbles, the combined use of laser vibrometry and finite element modelling supported a non-invasive measurement of the acoustic pressure and an enhanced understanding of the system resonances. Calibrated holographic optical tweezers were used for direct measurements of the acoustic forces acting on an isolated microbubble, at low driving pressures, and to confirm the spatial distribution of the acoustic field. This allowed quantitative acoustic pressure measurements by particle tracking, using polystyrene beads, and an evaluation of the related uncertainties. This process facilitated the extension of tracking to microbubbles, which have a negative acoustophoretic contrast factor, allowing acoustic force measurements on bubbles at higher pressures than optical tweezers, highlighting four peaks in the acoustic response of the device. Results and methodologies are relevant to acoustofluidic applications requiring a precise characterization of the acoustic field and, in general, to biomedical applications with microbubbles or deformable particles.
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Affiliation(s)
- Gianluca Memoli
- Department of Acoustics, National Physical Laboratory, Hampton Road, Teddington TW11 0LW, United Kingdom
| | - Christopher R Fury
- Department of Acoustics, National Physical Laboratory, Hampton Road, Teddington TW11 0LW, United Kingdom
| | - Kate O Baxter
- Department of Acoustics, National Physical Laboratory, Hampton Road, Teddington TW11 0LW, United Kingdom
| | - Pierre N Gélat
- Department of Acoustics, National Physical Laboratory, Hampton Road, Teddington TW11 0LW, United Kingdom
| | - Philip H Jones
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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48
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Jones PH, Shakdher S, Singh P. Synthesis maps: visual knowledge translation for the CanIMPACT clinical system and patient cancer journeys. ACTA ACUST UNITED AC 2017; 24:129-134. [PMID: 28490928 DOI: 10.3747/co.24.3452] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Salient findings and interpretations from the canimpact clinical cancer research study are visually represented in two synthesis maps for the purpose of communicating an integrated presentation of the study to clinical cancer researchers and policymakers. Synthesis maps integrate evidence and expertise into a visual narrative for knowledge translation and communication. A clinical system synthesis map represents the current Canadian primary care and cancer practice systems, proposed as a visual knowledge translation from the mixed-methods canimpact study to inform Canadian clinical research, policy, and practice discourses. Two synthesis maps, drawn together from multiple canimpact investigations and sources, were required to articulate critical differences between the clinical system and patient perspectives. The synthesis map of Canada-wide clinical cancer systems illustrates the relationships between primary care and the full cancer continuum. A patient-centred map was developed to represent the cancer (and primary care) journeys as experienced by breast and colorectal cancer patients.
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Affiliation(s)
- P H Jones
- Strategic Innovation Lab, ocad University, Strategic Innovation Lab, Toronto, ON
| | - S Shakdher
- Strategic Innovation Lab, ocad University, Strategic Innovation Lab, Toronto, ON
| | - P Singh
- Strategic Innovation Lab, ocad University, Strategic Innovation Lab, Toronto, ON
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49
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Liu Z, Jones PH. Optical manipulation using highly focused alternate radially and azimuthally polarized beams modulated by a devil's lens. J Opt Soc Am A Opt Image Sci Vis 2016; 33:2501-2508. [PMID: 27906277 DOI: 10.1364/josaa.33.002501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We propose and demonstrate a novel high numerical aperture (NA) focusing system composed of an annular beam with alternate radially and azimuthally polarized rings, focused by a devil's lens (DL), and further investigate its radiation forces acting upon a Rayleigh particle both analytically and numerically. Strongly focused cylindrical vector beams produce either dark-centered or peak-centered intensity distributions depending on the state of polarization, whereas the DL produces a series of foci along the propagation direction. We exploit these focusing properties and show that by selecting an appropriate truncation parameter in front of the focusing lens, the proposed optical focusing system can selectively trap and manipulate dielectric micro-particles with low or high refractive indices by simply adjusting the radius of the pupil or the beam. Finally, the stability conditions for effectively trapping and manipulating Rayleigh particles are analyzed. The results obtained in this work are of interest in possible applications in optical confinement and manipulation, sorting micro-particles, and making use of a DL.
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50
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Abstract
In this Letter, we demonstrate the formation of a stable two-dimensional lattice of colloidal particles in the interference pattern formed by four evanescent optical fields at a dielectric interface. The microspheres are observed to form a two-dimensional square lattice with lattice vectors inclined relative to the beam propagation directions. We use digital video microscopy and particle tracking to measure the Brownian motion of particles bound in the lattice, and use this to characterize fluctuations in the local ordering of particles using the bond orientational order parameter, the probability distribution of which is shown to be a chi-squared distribution. An explanation for the form of this distribution is presented in terms of fluctuations of the modes of a ring of particles connected by springs.
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