Multiplex Cytological Profiling Assay to Measure Diverse Cellular States

Computational methods for image-based profiling are under active development, but their success hinges on assays that can capture a wide range of phenotypes. We have developed a multiplex cytological profiling assay that “paints the cell” with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery

Gut Microbiome Perturbations Induced by Bacterial Infection Affect Arsenic Biotransformation

Exposure to arsenic affects large human populations worldwide and has been associated with a long list of human diseases, including skin, bladder, lung, and liver cancers, diabetes, and cardiovascular disorders. In addition, there are large individual differences in susceptibility to arsenic-induced diseases, which are frequently associated with different patterns of arsenic metabolism. Several underlying mechanisms, such as genetic polymorphisms and epigenetics, have been proposed, as these factors closely impact the individuals’ capacity to metabolize arsenic. In this context, the role of the gut microbiome in directly metabolizing arsenic and triggering systemic responses in diverse organs raises the possibility that perturbations of the gut microbial communities affect the spectrum of metabolized arsenic species and subsequent toxicological effects. In this study, we used an animal model with an altered gut microbiome induced by bacterial infection, 16S rRNA gene sequencing, and inductively coupled plasma mass spectrometry-based arsenic speciation to examine the effect of gut microbiome perturbations on the biotransformation of arsenic. Metagenomics sequencing revealed that bacterial infection significantly perturbed the gut microbiome composition in C57BL/6 mice, which in turn resulted in altered spectra of arsenic metabolites in urine, with inorganic arsenic species and methylated and thiolated arsenic being perturbed. These data clearly illustrated that gut microbiome phenotypes significantly affected arsenic metabolic reactions, including reduction, methylation, and thiolation. These findings improve our understanding of how infectious diseases and environmental exposure interact and may also provide novel insight regarding the gut microbiome composition as a new risk factor of individual susceptibility to environmental chemicals.National Institute of Environmental Health Sciences (Massachusetts Institute of Technology. Center for Environmental Health Sciences Grant P30 ES002109)National Institute of Environmental Health Sciences (University of North Carolina. Center for Environmental Health and Susceptibility Grant P30 ES010126

Recurrent structural variation, clustered sites of selection, and disease risk for the complement factor H (CFH) gene family

Data deposition: The data reported in this paper have been deposited as a National Center for Biotechnology Information BioProject (accession no. PRJNA401648). Author contributions: S.C. and E.E.E. designed research; S.C., C.B., L.H., K.P., K.M.M., M.S., A.E.W., V.D., T.A.G.-L., and R.K.W. performed research; S.C., J.H., C.B., L.H., K.P., K.M.M., M.S., A.E.W., V.D., F.G., A.J.R., R.H.G., T.A.G.-L., R.K.W., B.H.F.W., P.N.B., R.A., and E.E.E. contributed new reagents/analytic tools; S.C., B.J.N., J.H., and E.E.E. analyzed data; and S.C., B.J.N., and E.E.E. wrote the paper.Peer reviewedPublisher PD

Planning and optimising a digital intervention to protect older adults' cognitive health.

BackgroundBy 2050, worldwide dementia prevalence is expected to triple. Affordable, scalable interventions are required to support protective behaviours such as physical activity, cognitive training and healthy eating. This paper outlines the theory-, evidence- and person-based development of 'Active Brains': a multi-domain digital behaviour change intervention to reduce cognitive decline amongst older adults.MethodsDuring the initial planning phase, scoping reviews, consultation with PPI contributors and expert co-investigators and behavioural analysis collated and recorded evidence that was triangulated to inform provisional 'guiding principles' and an intervention logic model. The following optimisation phase involved qualitative think aloud and semi-structured interviews with 52 older adults with higher and lower cognitive performance scores. Data were analysed thematically and informed changes and additions to guiding principles, the behavioural analysis and the logic model which, in turn, informed changes to intervention content.ResultsScoping reviews and qualitative interviews suggested that the same intervention content may be suitable for individuals with higher and lower cognitive performance. Qualitative findings revealed that maintaining independence and enjoyment motivated engagement in intervention-targeted behaviours, whereas managing ill health was a potential barrier. Social support for engaging in such activities could provide motivation, but was not desirable for all. These findings informed development of intervention content and functionality that appeared highly acceptable amongst a sample of target users.ConclusionsA digitally delivered intervention with minimal support appears acceptable and potentially engaging to older adults with higher and lower levels of cognitive performance. As well as informing our own intervention development, insights obtained through this process may be useful for others working with, and developing interventions for, older adults and/or those with cognitive impairment

Clinical phenotypes of perinatal depression and time of symptom onset: analysis of data from an international consortium

Background The perinatal period is a time of high risk for onset of depressive disorders and is associated with substantial morbidity and mortality, including maternal suicide. Perinatal depression comprises a heterogeneous group of clinical subtypes, and further refinement is needed to improve treatment outcomes. We sought to empirically identify and describe clinically relevant phenotypic subtypes of perinatal depression, and further characterise subtypes by time of symptom onset within pregnancy and three post-partum periods. Methods Data were assembled from a subset of seven of 19 international sites in the Postpartum Depression: Action Towards Causes and Treatment (PACT) Consortium. In this analysis, the cohort was restricted to women aged 19–40 years with information about onset of depressive symptoms in the perinatal period and complete prospective data for the ten-item Edinburgh postnatal depression scale (EPDS). Principal components and common factor analysis were used to identify symptom dimensions in the EPDS. The National Institute of Mental Health research domain criteria functional constructs of negative valence and arousal were applied to the EPDS dimensions that reflect states of depressed mood, anhedonia, and anxiety. We used k-means clustering to identify subtypes of women sharing symptom patterns. Univariate and bivariate statistics were used to describe the subtypes. Findings Data for 663 women were included in these analyses. We found evidence for three underlying dimensions measured by the EPDS: depressed mood, anxiety, and anhedonia. On the basis of these dimensions, we identified five distinct subtypes of perinatal depression: severe anxious depression, moderate anxious depression, anxious anhedonia, pure anhedonia, and resolved depression. These subtypes have clear differences in symptom quality and time of onset. Anxiety and anhedonia emerged as prominent symptom dimensions with post-partum onset and were notably severe. Interpretation Our findings show that there might be different types and severity of perinatal depression with varying time of onset throughout pregnancy and post partum. These findings support the need for tailored treatments that improve outcomes for women with perinatal depression

The Active Brains Digital Intervention to Reduce Cognitive Decline in Older Adults: Protocol for a Feasibility Randomized Controlled Trial.

BACKGROUND: Increasing physical activity, improving diet, and performing brain training exercises are associated with reduced cognitive decline in older adults. OBJECTIVE: In this paper, we describe a feasibility trial of the Active Brains intervention, a web-based digital intervention developed to support older adults to make these 3 healthy behavior changes associated with improved cognitive health. The Active Brains trial is a randomized feasibility trial that will test how accessible, acceptable, and feasible the Active Brains intervention is and the effectiveness of the study procedures that we intend to use in the larger, main trial. METHODS: In the randomized controlled trial (RCT), we use a parallel design. We will be conducting the intervention with 2 populations recruited through GP practices (family practices) in England from 2018 to 2019: older adults with signs of cognitive decline and older adults without any cognitive decline. Trial participants were randomly allocated to 1 of 3 study groups: usual care, the Active Brains intervention, or the Active Brains website plus brief support from a trained coach (over the phone or by email). The main outcomes are performance on cognitive tasks, quality of life (using EuroQol-5D 5 level), Instrumental Activities of Daily Living, and diagnoses of dementia. Secondary outcomes (including depression, enablement, and health care costs) and process measures (including qualitative interviews with participants and supporters) will also be collected. The trial has been approved by the National Health Service Research Ethics Committee (reference 17/SC/0463). RESULTS: Results will be published in peer-reviewed journals, presented at conferences, and shared at public engagement events. Data collection was completed in May 2020, and the results will be reported in 2021. CONCLUSIONS: The findings of this study will help us to identify and make important changes to the website, the support received, or the study procedures before we progress to our main randomized phase III trial. TRIAL REGISTRATION: International Standard Randomized Controlled Trial Number 23758980; http://www.isrctn.com/ISRCTN23758980. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/18929

Controlled attenuation parameter in NAFLD identifies risk of suboptimal glycaemic and metabolic control

To examine the relationship between steatosis quantified by controlled attenuation parameter (CAP) values and glycaemic/metabolic control. 230 patients, recruited from an Endocrine clinic or primary care underwent routine Hepatology assessment, with liver stiffness measurements and simultaneous CAP. Multivariable logistic regression was performed to identify potential predictors of Metabolic Syndrome (MetS), HbA1c ≥ 7%, use of insulin, hypertriglyceridaemia and CAP ≥ 300 dB/m. Patients were 56.7 ± 12.3 years of age with a high prevalence of MetS (83.5%), T2DM (81.3%), and BMI ≥ 40 kg/m (18%). Median CAP score was 344 dB/m, ranging from 128 to 400 dB/m. BMI (aOR 1.140 95% CI 1.068-1.216), requirement for insulin (aOR 2.599 95% CI 1.212-5.575), and serum ALT (aOR 1.018 95% CI 1.004-1.033) were independently associated with CAP ≥ 300 dB/m. Patients with CAP interquartile range

Digital interventions for hypertension and asthma to support patient self-management in primary care: the DIPSS research programme including two RCTs

Background: Digital interventions offer a potentially cost-effective means to support patient self-management in primary care, but evidence for the feasibility, acceptability and cost-effectiveness of digital interventions remains mixed. This programme focused on the potential for self-management digital interventions to improve outcomes in two common, contrasting conditions (i.e. hypertension and asthma) for which care is currently suboptimal, leading to excess deaths, illness, disability and costs for the NHS. Objectives: The overall purpose was to address the question of how digital interventions can best provide cost-effective support for patient self-management in primary care. Our aims were to develop and trial digital interventions to support patient self-management of hypertension and asthma. Through the process of planning, developing and evaluating these interventions, we also aimed to generate a better understanding of what features and methods for implementing digital interventions could make digital interventions acceptable, feasible, effective and cost-effective to integrate into primary care. Design: For the hypertension strand, we carried out systematic reviews of quantitative and qualitative evidence, intervention planning, development and optimisation, and an unmasked randomised controlled trial comparing digital intervention with usual care, with a health economic analysis and nested process evaluation. For the asthma strand, we carried out a systematic review of quantitative evidence, intervention planning, development and optimisation, and a feasibility randomised controlled trial comparing digital intervention with usual care, with nested process evaluation. Setting: General practices (hypertension, n = 76; asthma, n = 7) across Wessex and Thames Valley regions in Southern England. Participants: For the hypertension strand, people with uncontrolled hypertension taking one, two or three antihypertensive medications. For the asthma strand, adults with asthma and impaired asthma-related quality of life. Interventions: Our hypertension intervention (i.e. HOME BP) was a digital intervention that included motivational training for patients to self-monitor blood pressure, as well as health-care professionals to support self-management; a digital interface to send monthly readings to the health-care professional and to prompt planned medication changes when patients’ readings exceeded recommended targets for 2 consecutive months; and support for optional patient healthy behaviour change (e.g. healthy diet/weight loss, increased physical activity and reduced alcohol and salt consumption). The control group were provided with a Blood Pressure UK (London, UK) leaflet for hypertension and received routine hypertension care. Our asthma intervention (i.e. My Breathing Matters) was a digital intervention to improve the functional quality of life of primary care patients with asthma by supporting illness self-management. Motivational content intended to facilitate use of pharmacological self-management strategies (e.g. medication adherence and appropriate health-care service use) and non-pharmacological self-management strategies (e.g. breathing retraining, stress reduction and healthy behaviour change). The control group were given an Asthma UK (London, UK) information booklet on asthma self-management and received routine asthma care. Main outcome measures: The primary outcome for the hypertension randomised controlled trial was difference between intervention and usual-care groups in mean systolic blood pressure (mmHg) at 12 months, adjusted for baseline blood pressure, blood pressure target (i.e. standard, diabetic or aged > 80 years), age and general practice. The primary outcome for the asthma feasibility study was the feasibility of the trial design, including recruitment, adherence, intervention engagement and retention at follow-up. Health-care utilisation data were collected via notes review. Review methods: The quantitative reviews included a meta-analysis. The qualitative review comprised a meta-ethnography. Results: A total of 622 hypertensive patients were recruited to the randomised controlled trial, and 552 (89%) were followed up at 12 months. Systolic blood pressure was significantly lower in the intervention group at 12 months, with a difference of –3.4 mmHg (95% confidence interval –6.1 to –0.8 mmHg), and this gave an incremental cost per unit of systolic blood pressure reduction of £11 (95% confidence interval £5 to £29). Owing to a cost difference of £402 and a quality-adjusted life-year (QALY) difference of 0.044, long-term modelling puts the incremental cost per QALY at just over £9000. The probability of being cost-effective was 66% at willingness to pay £20,000 per quality-adjusted life-year, and this was higher at higher thresholds. A total of 88 patients were recruited to the asthma feasibility trial (target n = 80; n = 44 in each arm). At 3-month follow-up, two patients withdrew and six patients did not complete outcome measures. At 12 months, two patients withdrew and four patients did not complete outcome measures. A total of 36 out of 44 patients in the intervention group engaged with My Breathing Matters [with a median of four (range 0–25) logins]

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN