• Concordance and timing in recording cancer events in primary care, hospital and mortality records for patients with and without psoriasis: A population-based cohort study

      editor: Ramagopalan, Sreeram V.; Trafford, Alex M.; orcid: 0000-0001-8145-8133; email: alex.trafford@postgrad.manchester.ac.uk; Parisi, Rosa; Rutter, Martin K.; Kontopantelis, Evangelos; Griffiths, Christopher E. M.; Ashcroft, Darren M.; orcid: 0000-0002-2958-915X; on behalf of the Global Psoriasis Atlas (GPA) (Public Library of Science, 2021-07-19)
      Background: The association between psoriasis and the risk of cancer has been investigated in numerous studies utilising electronic health records (EHRs), with conflicting results in the extent of the association. Objectives: To assess concordance and timing of cancer recording between primary care, hospital and death registration data for people with and without psoriasis. Methods: Cohort studies delineated using primary care EHRs from the Clinical Practice Research Datalink (CPRD) GOLD and Aurum databases, with linkage to hospital episode statistics (HES), Office for National Statistics (ONS) mortality data and indices of multiple deprivation (IMD). People with psoriasis were matched to those without psoriasis by age, sex and general practice. Cancer recording between databases was investigated by proportion concordant, that being the presence of cancer record in both source and comparator datasets. Delay in recording cancer diagnoses between CPRD and HES records and predictors of discordance were also assessed. Results: 58,904 people with psoriasis and 350,592 comparison patients were included using CPRD GOLD; whereas 213,400 people with psoriasis and 1,268,998 comparison patients were included in CPRD Aurum. For all cancer records (excluding keratinocyte), concordance between CPRD and HES was greater than 80%. Concordance for same-site cancer records was markedly lower (<68% GOLD-linked data; <72% Aurum-linked data). Concordance of non-Hodgkin lymphoma and liver cancer recording between CPRD and HES was lower for people with psoriasis compared to those without. Conclusions: Concordance between CPRD and HES is poor when restricted to cancers of the same site, with greater discordance in people with psoriasis for some cancers of specific sites. The use of linked patient-level data is an important step in reducing misclassification of cancer outcomes in epidemiological studies using routinely collected electronic health records.
    • Discovery of re-purposed drugs that slow SARS-CoV-2 replication in human cells

      editor: Pekosz, Andrew; Pickard, Adam; orcid: 0000-0001-9757-143X; email: adam.pickard@manchester.ac.uk; Calverley, Ben C.; orcid: 0000-0001-9403-0363; Chang, Joan; orcid: 0000-0002-7283-9759; Garva, Richa; orcid: 0000-0001-7752-8936; Gago, Sara; Lu, Yinhui; Kadler, Karl E.; orcid: 0000-0003-4977-4683; email: karl.kadler@manchester.ac.uk (Public Library of Science, 2021-09-09)
      COVID-19 vaccines based on the Spike protein of SARS-CoV-2 have been developed that appear to be largely successful in stopping infection. However, therapeutics that can help manage the disease are still required until immunity has been achieved globally. The identification of repurposed drugs that stop SARS-CoV-2 replication could have enormous utility in stemming the disease. Here, using a nano-luciferase tagged version of the virus (SARS-CoV-2-ΔOrf7a-NLuc) to quantitate viral load, we evaluated a range of human cell types for their ability to be infected and support replication of the virus, and performed a screen of 1971 FDA-approved drugs. Hepatocytes, kidney glomerulus, and proximal tubule cells were particularly effective in supporting SARS-CoV-2 replication, which is in-line with reported proteinuria and liver damage in patients with COVID-19. Using the nano-luciferase as a measure of virus replication we identified 35 drugs that reduced replication in Vero cells and human hepatocytes when treated prior to SARS-CoV-2 infection and found amodiaquine, atovaquone, bedaquiline, ebastine, LY2835219, manidipine, panobinostat, and vitamin D3 to be effective in slowing SARS-CoV-2 replication in human cells when used to treat infected cells. In conclusion, our study has identified strong candidates for drug repurposing, which could prove powerful additions to the treatment of COVID.
    • Electronic and electrochemical viral detection for point-of-care use: A systematic review

      editor: Maheshwari, Vivek; Monteil, Solen; orcid: 0000-0002-0891-2624; Casson, Alexander J.; Jones, Samuel T.; orcid: 0000-0002-3907-0810; email: samuel.jones-4@manchester.ac.uk (Public Library of Science, 2021-09-30)
      Detecting viruses, which have significant impact on health and the economy, is essential for controlling and combating viral infections. In recent years there has been a focus towards simpler and faster detection methods, specifically through the use of electronic-based detection at the point-of-care. Point-of-care sensors play a particularly important role in the detection of viruses. Tests can be performed in the field or in resource limited regions in a simple manner and short time frame, allowing for rapid treatment. Electronic based detection allows for speed and quantitative detection not otherwise possible at the point-of-care. Such approaches are largely based upon voltammetry, electrochemical impedance spectroscopy, field effect transistors, and similar electrical techniques. Here, we systematically review electronic and electrochemical point-of-care sensors for the detection of human viral pathogens. Using the reported limits of detection and assay times we compare approaches both by detection method and by the target analyte of interest. Compared to recent scoping and narrative reviews, this systematic review which follows established best practice for evidence synthesis adds substantial new evidence on 1) performance and 2) limitations, needed for sensor uptake in the clinical arena. 104 relevant studies were identified by conducting a search of current literature using 7 databases, only including original research articles detecting human viruses and reporting a limit of detection. Detection units were converted to nanomolars where possible in order to compare performance across devices. This approach allows us to identify field effect transistors as having the fastest median response time, and as being the most sensitive, some achieving single-molecule detection. In general, we found that antigens are the quickest targets to detect. We also observe however, that reports are highly variable in their chosen metrics of interest. We suggest that this lack of systematisation across studies may be a major bottleneck in sensor development and translation. Where appropriate, we use the findings of the systematic review to give recommendations for best reporting practice.
    • Fungal and host protein persulfidation are functionally correlated and modulate both virulence and antifungal response

      editor: Heitman, Joseph; Sueiro-Olivares, Monica; Scott, Jennifer; Gago, Sara; orcid: 0000-0002-7027-4598; Petrovic, Dunja; Kouroussis, Emilia; Zivanovic, Jasmina; Yu, Yidong; Strobel, Marlene; Cunha, Cristina; orcid: 0000-0002-6002-5782; et al. (Public Library of Science, 2021-06-01)
      Aspergillus fumigatus is a human fungal pathogen that can cause devastating pulmonary infections, termed “aspergilloses,” in individuals suffering immune imbalances or underlying lung conditions. As rapid adaptation to stress is crucial for the outcome of the host–pathogen interplay, here we investigated the role of the versatile posttranslational modification (PTM) persulfidation for both fungal virulence and antifungal host defense. We show that an A. fumigatus mutant with low persulfidation levels is more susceptible to host-mediated killing and displays reduced virulence in murine models of infection. Additionally, we found that a single nucleotide polymorphism (SNP) in the human gene encoding cystathionine γ-lyase (CTH) causes a reduction in cellular persulfidation and correlates with a predisposition of hematopoietic stem cell transplant recipients to invasive pulmonary aspergillosis (IPA), as correct levels of persulfidation are required for optimal antifungal activity of recipients’ lung resident host cells. Importantly, the levels of host persulfidation determine the levels of fungal persulfidation, ultimately reflecting a host–pathogen functional correlation and highlighting a potential new therapeutic target for the treatment of aspergillosis.
    • IVEN: A quantitative tool to describe 3D cell position and neighbourhood reveals architectural changes in FGF4-treated preimplantation embryos

      editor: Brickman, Joshua Mark; Forsyth, Jessica E.; orcid: 0000-0002-5839-9160; Al-Anbaki, Ali H.; de la Fuente, Roberto; orcid: 0000-0002-7567-032X; Modare, Nikkinder; orcid: 0000-0001-5417-5795; Perez-Cortes, Diego; Rivera, Isabel; orcid: 0000-0002-2026-3428; Seaton Kelly, Rowena; orcid: 0000-0002-0183-9954; Cotter, Simon; orcid: 0000-0001-5974-7393; Plusa, Berenika; orcid: 0000-0003-2214-5940; email: berenika.plusa@manchester.ac.uk (Public Library of Science, 2021-07-26)
      Architectural changes at the cellular and organism level are integral and necessary to successful development and growth. During mammalian preimplantation development, cells reduce in size and the architecture of the embryo changes significantly. Such changes must be coordinated correctly to ensure continued development of the embryo and, ultimately, a successful pregnancy. However, the nature of such transformations is poorly defined during mammalian preimplantation development. In order to quantitatively describe changes in cell environment and organism architecture, we designed Internal Versus External Neighbourhood (IVEN). IVEN is a user-interactive, open-source pipeline that classifies cells into different populations based on their position and quantifies the number of neighbours of every cell within a dataset in a 3D environment. Through IVEN-driven analyses, we show how transformations in cell environment, defined here as changes in cell neighbourhood, are related to changes in embryo geometry and major developmental events during preimplantation mammalian development. Moreover, we demonstrate that modulation of the FGF pathway alters spatial relations of inner cells and neighbourhood distributions, leading to overall changes in embryo architecture. In conjunction with IVEN-driven analyses, we uncover differences in the dynamic of cell size changes over the preimplantation period and determine that cells within the mammalian embryo initiate growth phase only at the time of implantation.
    • Non-territorial GPS-tagged golden eagles Aquila chrysaetos at two Scottish wind farms: Avoidance influenced by preferred habitat distribution, wind speed and blade motion status

      editor: Magar, Vanesa; Fielding, Alan H.; Anderson, David; Benn, Stuart; Dennis, Roy; Geary, Matthew; Weston, Ewan; Whitfield, D. Philip; orcid: 0000-0003-4255-7782; email: phil.whitfield@natural-research.org (Public Library of Science, 2021-08-05)
      Wind farms can have two broad potential adverse effects on birds via antagonistic processes: displacement from the vicinity of turbines (avoidance), or death through collision with rotating turbine blades. These effects may not be mutually exclusive. Using detailed data from 99 turbines at two wind farms in central Scotland and thousands of GPS-telemetry data from dispersing golden eagles, we tested three hypotheses. Before-and-after-operation analyses supported the hypothesis of avoidance: displacement was reduced at turbine locations in more preferred habitat and with more preferred habitat nearby. After-operation analyses (i.e. from the period when turbines were operational) showed that at higher wind speeds and in highly preferred habitat eagles were less wary of turbines with motionless blades: rejecting our second hypothesis. Our third hypothesis was supported, since at higher wind speeds eagles flew closer to operational turbines; especially–once more–turbines in more preferred habitat. After operation, eagles effectively abandoned inner turbine locations, and flight line records close to rotor blades were rare. While our study indicated that whole-wind farm functional habitat loss through avoidance was the substantial adverse impact, we make recommendations on future wind farm design to minimise collision risk further. These largely entail developers avoiding outer turbine locations which are in and surrounded by swathes of preferred habitat. Our study illustrates the insights which detailed case studies of large raptors at wind farms can bring and emphasises that the balance between avoidance and collision can have several influences.
    • Tau, XMAP215/Msps and Eb1 co-operate interdependently to regulate microtubule polymerisation and bundle formation in axons

      editor: Yu, Fengwei; Hahn, Ines; orcid: 0000-0001-7703-8160; email: Ines.Hahn@manchester.ac.uk; Voelzmann, Andre; orcid: 0000-0002-7682-5637; Parkin, Jill; Fülle, Judith B.; orcid: 0000-0003-1609-1368; Slater, Paula G.; orcid: 0000-0003-2601-0613; Lowery, Laura Anne; orcid: 0000-0001-8959-2679; Sanchez-Soriano, Natalia; orcid: 0000-0002-6667-2817; email: N.Sanchez-Soriano@liverpool.ac.uk; Prokop, Andreas; email: Andreas.Prokop@manchester.ac.uk (Public Library of Science, 2021-07-06)
      The formation and maintenance of microtubules requires their polymerisation, but little is known about how this polymerisation is regulated in cells. Focussing on the essential microtubule bundles in axons of Drosophila and Xenopus neurons, we show that the plus-end scaffold Eb1, the polymerase XMAP215/Msps and the lattice-binder Tau co-operate interdependently to promote microtubule polymerisation and bundle organisation during axon development and maintenance. Eb1 and XMAP215/Msps promote each other’s localisation at polymerising microtubule plus-ends. Tau outcompetes Eb1-binding along microtubule lattices, thus preventing depletion of Eb1 tip pools. The three factors genetically interact and show shared mutant phenotypes: reductions in axon growth, comet sizes, comet numbers and comet velocities, as well as prominent deterioration of parallel microtubule bundles into disorganised curled conformations. This microtubule curling is caused by Eb1 plus-end depletion which impairs spectraplakin-mediated guidance of extending microtubules into parallel bundles. Our demonstration that Eb1, XMAP215/Msps and Tau co-operate during the regulation of microtubule polymerisation and bundle organisation, offers new conceptual explanations for developmental and degenerative axon pathologies.
    • Ten simple rules for teaching applied programming in an authentic and immersive online environment

      editor: Schwartz, Russell; Hooley, Frances; orcid: 0000-0003-1048-4558; Freeman, Peter J.; orcid: 0000-0002-5838-5404; Davies, Angela C.; orcid: 0000-0002-3365-7231; email: angela.davies@manchester.ac.uk (Public Library of Science, 2021-08-05)
    • Trichuris muris infection drives cell-intrinsic IL4R alpha independent colonic RELMα+ macrophages

      editor: Nair, Meera Goh; Forman, Ruth; orcid: 0000-0003-0374-6679; email: ruth.forman@manchester.ac.uk; Logunova, Larisa; orcid: 0000-0002-7601-8296; Smith, Hannah; orcid: 0000-0001-8911-9048; Wemyss, Kelly; orcid: 0000-0003-0385-5920; Mair, Iris; Boon, Louis; Allen, Judith E.; orcid: 0000-0002-3829-066X; Muller, Werner; orcid: 0000-0002-1297-9725; Pennock, Joanne L.; orcid: 0000-0002-8304-2905; et al. (Public Library of Science, 2021-07-30)
      The intestinal nematode parasite Trichuris muris dwells in the caecum and proximal colon driving an acute resolving intestinal inflammation dominated by the presence of macrophages. Notably, these macrophages are characterised by their expression of RELMα during the resolution phase of the infection. The RELMα+ macrophage phenotype associates with the presence of alternatively activated macrophages and work in other model systems has demonstrated that the balance of classically and alternatively activated macrophages is critically important in enabling the resolution of inflammation. Moreover, in the context of type 2 immunity, RELMα+ alternatively activated macrophages are associated with the activation of macrophages via the IL4Rα. Despite a breadth of inflammatory pathologies associated with the large intestine, including those that accompany parasitic infection, it is not known how colonic macrophages are activated towards an alternatively activated phenotype. Here, we address this important knowledge gap by using Trichuris muris infection, in combination with transgenic mice (IL4Rαfl/fl.CX3CR1Cre) and IL4Rα-deficient/wild-type mixed bone marrow chimaeras. We make the unexpected finding that education of colonic macrophages towards a RELMα+, alternatively activated macrophage phenotype during T. muris infection does not require IL4Rα expression on macrophages. Further, this independence is maintained even when the mice are treated with an anti-IFNγ antibody during infection to create a strongly polarised Th2 environment. In contrast to RELMα, PD-L2 expression on macrophages post infection was dependent on IL4Rα signalling in the macrophages. These novel data sets are important, revealing a surprising cell-intrinsic IL4R alpha independence of the colonic RELMα+ alternatively activated macrophage during Trichuris muris infection.