Transfer learning with graph neural networks for improved molecular property prediction in the multi-fidelity setting.

We investigate the potential of graph neural networks for transfer learning and improving molecular property prediction on sparse and expensive to acquire high-fidelity data by leveraging low-fidelity measurements as an inexpensive proxy for a targeted property of interest. This problem arises in discovery processes that rely on screening funnels for trading off the overall costs against throughput and accuracy. Typically, individual stages in these processes are loosely connected and each one generates data at different scale and fidelity. We consider this setup holistically and demonstrate empirically that existing transfer learning techniques for graph neural networks are generally unable to harness the information from multi-fidelity cascades. Here, we propose several effective transfer learning strategies and study them in transductive and inductive settings. Our analysis involves a collection of more than 28 million unique experimental protein-ligand interactions across 37 targets from drug discovery by high-throughput screening and 12 quantum properties from the dataset QMugs. The results indicate that transfer learning can improve the performance on sparse tasks by up to eight times while using an order of magnitude less high-fidelity training data. Moreover, the proposed methods consistently outperform existing transfer learning strategies for graph-structured data on drug discovery and quantum mechanics datasets.

Effect of COVID-19 on Bronchiectasis Exacerbation Rates: A Retrospective U.S. Insurance Claims Study.

Rationale: Bronchiectasis is a chronic, progressive disease of bronchial dilation, inflammation, and scarring leading to impaired mucociliary clearance and increased susceptibility to infection. Identified causes include previous severe respiratory infections. A small, single-center UK study demonstrated a reduction in bronchiectasis exacerbations during the first year of the coronavirus disease (COVID-19) pandemic. No studies have been conducted in a U.S. (commercially insured) cohort to date. Objectives: To explore the impact of the COVID-19 pandemic on the frequency of exacerbations in a large cohort of commercially insured U.S. patients with bronchiectasis by testing the hypothesis that U.S. patients with bronchiectasis had fewer exacerbations during the pandemic. Methods: This retrospective observational cohort study used health insurance claims data from Optum's deidentified Clinformatics Data Mart database, which included U.S. patients and their covered dependents. Eligible patients were ⩾18 years of age with bronchiectasis; patients with other respiratory conditions were excluded. The main study cohort excluded patients with frequent asthma and/or chronic obstructive pulmonary disease diagnoses. The primary objective was to compare the bronchiectasis exacerbation rates before and during the COVID-19 pandemic. Results: The median number of exacerbations per patient per year decreased significantly from the year before the COVID-19 pandemic to the first year of the pandemic (1 vs. 0; P < 0.01). More patients had zero exacerbations during the first year of the pandemic than the year prior (57% vs. 24%; McNemar's chi-square = 122.56; P < 0.01). Conclusions: In a U.S. population-based study of patients with International Classification of Diseases codes for bronchiectasis, the rate of exacerbations during Year 1 of the COVID-19 pandemic was reduced compared with the 2-year time period preceding the pandemic.

Evaluating clinical outcomes and prognosis in patients with cirrhosis and portal hypertension: a retrospective observational cohort study.

OBJECTIVE: Cirrhosis describes the end-stage of chronic liver disease. Irreversible changes in the liver cause portal hypertension, which can progress to serious complications and death. Only a few studies with small sample sizes have investigated the prognosis of cirrhosis with portal hypertension. We used electronic healthcare records to examine liver-related outcomes in patients with diagnosed/suspected portal hypertension. DESIGN: This retrospective observational cohort study used secondary health data between 1 January 2017 and 3 December 2020 from the TriNetX Network, a federated electronic healthcare records platform. Three patient groups with cirrhosis and diagnosed/suspected portal hypertension were identified ('most severe', 'moderate severity' and 'least severe'). Outcomes studied individually and as a composite were variceal haemorrhage, hepatic encephalopathy, complications of ascites and recorded mortality up to 24 months. RESULTS: There were 13 444, 23 299, and 23 836 patients in the most severe, moderate severity and least severe groups, respectively. Mean age was similar across groups; most participants were white. The most common individual outcomes at 24 months were variceal haemorrhage in the most severe group, recorded mortality and hepatic encephalopathy in the moderate severity group, and recorded mortality in the least severe group. Recorded mortality rate was similar across groups. For the composite outcome, cumulative incidence was 59% in the most severe group at 6 months. Alcohol-associated liver disease and metabolic-associated steatohepatitis were significantly associated with the composite outcome across groups. CONCLUSION: Our analysis of a large dataset from electronic healthcare records illustrates the poor prognosis of patients with diagnosed/suspected portal hypertension.

Modelling local and general quantum mechanical properties with attention-based pooling.

Atom-centred neural networks represent the state-of-the-art for approximating the quantum chemical properties of molecules, such as internal energies. While the design of machine learning architectures that respect chemical principles has continued to advance, the final atom pooling operation that is necessary to convert from atomic to molecular representations in most models remains relatively undeveloped. The most common choices, sum and average pooling, compute molecular representations that are naturally a good fit for many physical properties, while satisfying properties such as permutation invariance which are desirable from a geometric deep learning perspective. However, there are growing concerns that such simplistic functions might have limited representational power, while also being suboptimal for physical properties that are highly localised or intensive. Based on recent advances in graph representation learning, we investigate the use of a learnable pooling function that leverages an attention mechanism to model interactions between atom representations. The proposed pooling operation is a drop-in replacement requiring no changes to any of the other architectural components. Using SchNet and DimeNet++ as starting models, we demonstrate consistent uplifts in performance compared to sum and mean pooling and a recent physics-aware pooling operation designed specifically for orbital energies, on several datasets, properties, and levels of theory, with up to 85% improvements depending on the specific task.

MF-PCBA: Multifidelity High-Throughput Screening Benchmarks for Drug Discovery and Machine Learning.

High-throughput screening (HTS), as one of the key techniques in drug discovery, is frequently used to identify promising drug candidates in a largely automated and cost-effective way. One of the necessary conditions for successful HTS campaigns is a large and diverse compound library, enabling hundreds of thousands of activity measurements per project. Such collections of data hold great promise for computational and experimental drug discovery efforts, especially when leveraged in combination with modern deep learning techniques, and can potentially lead to improved drug activity predictions and cheaper and more effective experimental design. However, existing collections of machine-learning-ready public datasets do not exploit the multiple data modalities present in real-world HTS projects. Thus, the largest fraction of experimental measurements, corresponding to hundreds of thousands of "noisy" activity values from primary screening, are effectively ignored in the majority of machine learning models of HTS data. To address these limitations, we introduce Multifidelity PubChem BioAssay (MF-PCBA), a curated collection of 60 datasets that includes two data modalities for each dataset, corresponding to primary and confirmatory screening, an aspect that we call multifidelity. Multifidelity data accurately reflect real-world HTS conventions and present a new, challenging task for machine learning: the integration of low- and high-fidelity measurements through molecular representation learning, taking into account the orders-of-magnitude difference in size between the primary and confirmatory screens. Here we detail the steps taken to assemble MF-PCBA in terms of data acquisition from PubChem and the filtering steps required to curate the raw data. We also provide an evaluation of a recent deep-learning-based method for multifidelity integration across the introduced datasets, demonstrating the benefit of leveraging all HTS modalities, and a discussion in terms of the roughness of the molecular activity landscape. In total, MF-PCBA contains over 16.6 million unique molecule-protein interactions. The datasets can be easily assembled by using the source code available at https://github.com/davidbuterez/mf-pcba.

Inhaled Corticosteroid Withdrawal and Change in Lung Function in Primary Care Patients with Chronic Obstructive Pulmonary Disease in England.

Rationale: In chronic obstructive pulmonary disease (COPD), inhaled corticosteroids (ICS) are associated with pneumonia, highlighting the importance of investigating subgroups of patients who may benefit from prolonged ICS use. Despite this, the WISDOM (Withdrawal of Inhaled Steroids during Optimized Bronchodilator Management) trial found a greater decline in forced expiratory volume in 1 second (FEV1) in patients with COPD who withdrew from ICS compared with patients who remained on triple therapy. Objectives: We investigated the association between ICS withdrawal and the rate of FEV1 decline in patients with COPD using routinely collected electronic healthcare records. Methods: Using CPRD (Clinical Practice Research Datalink) Aurum and Hospital episode statistics, we included patients with COPD who had been on triple therapy for at least 4 months. Patients were categorized into those who withdrew from ICS and those who remained on triple therapy during follow-up. Three cohorts were created: 1) patients meeting the WISDOM trial eligibility criteria; 2) patients with COPD not restricted by the WISDOM trial eligibility criteria; and 3) patients who would have been excluded from the WISDOM trial on the basis of their comorbidities. Mixed linear regression was used to model the association between ICS withdrawal and the rate of FEV1 decline (ml/year) adjusted for baseline characteristics. Results: A total of 6,008 patients with COPD met the WISDOM eligibility criteria, of which 9.0% withdrew from ICS. Mean rates of FEV1 declined -7.8 ml/year (95% confidence interval [CI], -19.7 to 4.1) for withdrawers and -15.2 ml/year (95% CI, -18.7 to -11.8) for those who remained on triple therapy (difference, P = 0.264). A total of 60,645 patients with COPD were not restricted by the WISDOM eligibility criteria. The mean rate of FEV1 decline was -32.6 ml/year (95% CI, -33.6 to -31.5) for withdrawers and -36.4 ml/year (95% CI, -39.4 to -33.4) for those who remained on triple therapy. A total of 32,882 patients with COPD were included in the last population representing those who would have been excluded from the WISDOM trial because of their comorbidities. The mean rate of FEV1 decline was -29.4 ml/year (95% CI, -30 to -28.1) in withdrawers and -31.3 ml/year (95% CI, -35 to -27.5) in those who remained on triple therapy. Conclusions: The rate of FEV1 decline was similar between patients on triple therapy and patients who withdrew from ICS regardless of the specific COPD population studied. In routine clinical practice, few patients with COPD meet WISDOM eligibility criteria, and few patients are withdrawn from ICS.

Challenges and Pitfalls of Using Repeat Spirometry Recordings in Routine Primary Care Data to Measure FEV1 Decline in a COPD Population.

BACKGROUND: Electronic healthcare records (EHR) are increasingly used in epidemiological studies but are often viewed as lacking quality compared to randomised control trials and prospective cohorts. Studies of patients with chronic obstructive pulmonary disease (COPD) often use the rate of forced expiratory volume in 1 second (FEV1) decline as an outcome; however, its definition and robustness in EHR have not been investigated. We aimed to investigate how the rate of FEV1 decline differs by the criteria used in an EHR database. METHODS: Clinical Practice Research Datalink and Hospital Episode Statistics were used. Patient populations were defined using 8 sets of criteria around repeated FEV1 measurements. At a minimum, patients had a diagnosis of COPD, were ≥35 years old, were current or ex-smokers, and had data recorded from 2004. FEV1 measurements recorded during follow-up were identified. Thereafter, eight populations were defined based on criteria around: i) the exclusion of patients or individual measurements with potential measurement error; ii) minimum number of FEV1 measurements; iii) minimum time interval between measurements; iv) specific timing of measurements; v) minimum follow-up time; and vi) the use of linked data. For each population, the rate of FEV1 decline was estimated using mixed linear regression. RESULTS: For 7/8 patient populations, rates of FEV1 decline (age and sex adjusted) were similar and ranged from -18.7mL/year (95% CI -19.2 to -18.2) to -16.5mL/year (95% CI -17.3 to -15.7). Rates of FEV1 decline in populations that excluded patients with potential measurement error ranged from -79.4mL/year (95% CI -80.7 to -78.2) to -46.8mL/year (95% CI -47.6 to -46.0). CONCLUSION: FEV1 decline remained similar in a COPD population regardless of number of FEV1 measurements, time intervals between measurements, follow-up period, exclusion of specific FEV1 measurements, and linkage to HES. However, exclusion of individuals with questionable data led to selection bias and faster rates of decline.

Accelerated FEV1 decline and risk of cardiovascular disease and mortality in a primary care population of COPD patients.

Accelerated lung function decline has been associated with increased risk of cardiovascular disease (CVD) in a general population, but little is known about this association in chronic obstructive pulmonary disease (COPD). We investigated the association between accelerated lung function decline and CVD outcomes and mortality in a primary care COPD population.COPD patients without a history of CVD were identified in the Clinical Practice Research Datalink (CPRD)-GOLD primary care dataset (n=36 382). Accelerated decline in forced expiratory volume in 1 s (FEV1) was defined using the fastest quartile of the COPD population's decline. A Cox regression was used to assess the association between baseline accelerated FEV1 decline and a composite CVD outcome over follow-up (myocardial infarction, ischaemic stroke, heart failure, atrial fibrillation, coronary artery disease and CVD mortality). The model was adjusted for age, sex, smoking status, body mass index, history of asthma, hypertension, diabetes, statin use, Modified Medical Research Council (mMRC) dyspnoea score, exacerbation frequency and baseline FEV1 % predicted.6110 COPD patients (16.8%) had a CVD event during follow-up; median length of follow-up was 3.6 years (interquartile range (IQR) 1.7-6.1 years). Median rate of FEV1 decline was -19.4 mL·year-1 (IQR -40.5-1.9); 9095 patients (25%) had accelerated FEV1 decline (> -40.5 mL·year-1), 27 287 (75%) did not (≤ -40.5 mL·year-1). Risk of CVD and mortality was similar between patients with and without accelerated FEV1 decline (HRadj 0.98, 95% CI 0.90-1.06). Corresponding risk estimates were 0.99 (95% CI 0.83-1.20) for heart failure, 0.89 (95% CI 0.70-1.12) for myocardial infarction, 1.01 (95% CI 0.82-1.23) for stroke, 0.97 (95% CI 0.81-1.15) for atrial fibrillation, 1.02 (95% CI 0.87-1.19) for coronary artery disease and 0.94 (95% CI 0.71-1.25) for CVD mortality. Rather, risk of CVD was associated with a mMRC score ≤2 and two or more exacerbations in the year prior.CVD outcomes and mortality were associated with exacerbation frequency and severity and increased mMRC dyspnoea score but not with accelerated FEV1 decline.

Characteristics Associated with Accelerated Lung Function Decline in a Primary Care Population with Chronic Obstructive Pulmonary Disease.

Background: Estimates for lung function decline in chronic obstructive pulmonary disease (COPD) have differed by study setting and have not been described in a UK primary care population. Purpose: To describe rates of FEV1 and FVC decline in COPD and investigate characteristics associated with accelerated decline. Patients and Methods: Current/ex-smoking COPD patients (35 years+) who had at least 2 FEV1 or FVC measurements ≥6 months apart were included using Clinical Practice Research Datalink. Patients were followed up for a maximum of 13 years. Accelerated rate of lung function decline was defined as the fastest quartile of decline using mixed linear regression, and association with baseline characteristics was investigated using logistic regression. Results: A total of 72,683 and 50,649 COPD patients had at least 2 FEV1 or FVC measurements, respectively. Median rates of FEV1 and FVC changes or decline were -18.1mL/year (IQR: -31.6 to -6.0) and -22.7mL/year (IQR: -39.9 to -6.7), respectively. Older age, high socioeconomic status, being underweight, high mMRC dyspnoea and frequent AECOPD or severe AECOPD were associated with an accelerated rate of FEV1 and FVC decline. Current smoking, mild airflow obstruction and inhaled corticosteroid treatment were additionally associated with accelerated FEV1 decline whilst women, sputum production and severe airflow obstruction were associated with accelerated FVC decline. Conclusion: Rate of FEV1 and FVC decline was similar and showed similar heterogeneity. Whilst FEV1 and FVC shared associations with baseline characteristics, a few differences highlighted the importance of both lung function measures in COPD progression. We identified important characteristics that should be monitored for disease progression.

Prediction of five-year mortality after COPD diagnosis using primary care records.

Accurate prognosis information after a diagnosis of chronic obstructive pulmonary disease (COPD) would facilitate earlier and better informed decisions about the use of prevention strategies and advanced care plans. We therefore aimed to develop and validate an accurate prognosis model for incident COPD cases using only information present in general practitioner (GP) records at the point of diagnosis. Incident COPD patients between 2004-2012 over the age of 35 were studied using records from 396 general practices in England. We developed a model to predict all-cause five-year mortality at the point of COPD diagnosis, using 47,964 English patients. Our model uses age, gender, smoking status, body mass index, forced expiratory volume in 1-second (FEV1) % predicted and 16 co-morbidities (the same number as the Charlson Co-morbidity Index). The performance of our chosen model was validated in all countries of the UK (N = 48,304). Our model performed well, and performed consistently in validation data. The validation area under the curves in each country varied between 0.783-0.809 and the calibration slopes between 0.911-1.04. Our model performed better in this context than models based on the Charlson Co-morbidity Index or Cambridge Multimorbidity Score. We have developed and validated a model that outperforms general multimorbidity scores at predicting five-year mortality after COPD diagnosis. Our model includes only data routinely collected before COPD diagnosis, allowing it to be readily translated into clinical practice, and has been made available through an online risk calculator (https://skiddle.shinyapps.io/incidentcopdsurvival/).

Dysregulated Antibody, Natural Killer Cell and Immune Mediator Profiles in Autoimmune Thyroid Diseases.

The pathogenesis of autoimmune thyroid diseases (AITD) is poorly understood and the association between different immune features and the germline variants involved in AITD are yet unclear. We previously observed systemic depletion of IgG core fucosylation and antennary α1,2 fucosylation in peripheral blood mononuclear cells in AITD, correlated with anti-thyroid peroxidase antibody (TPOAb) levels. Fucose depletion is known to potentiate strong antibody-mediated NK cell activation and enhanced target antigen-expressing cell killing. In autoimmunity, this may translate to autoantibody-mediated immune cell recruitment and attack of self-antigen expressing normal tissues. Hence, we investigated the crosstalk between immune cell traits, secreted proteins, genetic variants and the glycosylation patterns of serum IgG, in a multi-omic and cross-sectional study of 622 individuals from the TwinsUK cohort, 172 of whom were diagnosed with AITD. We observed associations between two genetic variants (rs505922 and rs687621), AITD status, the secretion of Desmoglein-2 protein, and the profile of two IgG N-glycan traits in AITD, but further studies need to be performed to better understand their crosstalk in AITD. On the other side, enhanced afucosylated IgG was positively associated with activatory CD335- CD314+ CD158b+ NK cell subsets. Increased levels of the apoptosis and inflammation markers Caspase-2 and Interleukin-1α positively associated with AITD. Two genetic variants associated with AITD, rs1521 and rs3094228, were also associated with altered expression of the thyrocyte-expressed ligands known to recognize the NK cell immunoreceptors CD314 and CD158b. Our analyses reveal a combination of heightened Fc-active IgG antibodies, effector cells, cytokines and apoptotic signals in AITD, and AITD genetic variants associated with altered expression of thyrocyte-expressed ligands to NK cell immunoreceptors. Together, TPOAb responses, dysregulated immune features, germline variants associated with immunoactivity profiles, are consistent with a positive autoreactive antibody-dependent NK cell-mediated immune response likely drawn to the thyroid gland in AITD.

Author Correction: Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer's disease risk.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Inhaled corticosteroids and FEV1 decline in chronic obstructive pulmonary disease: a systematic review.

Rate of FEV1 decline in COPD is heterogeneous and the extent to which inhaled corticosteroids (ICS) influence the rate of decline is unclear. The majority of previous reviews have investigated specific ICS and non-ICS inhalers and have consisted of randomised control trials (RCTs), which have specific inclusion and exclusion criteria and short follow up times. We aimed to investigate the association between change in FEV1 and ICS-containing medications in COPD patients over longer follow up times.MEDLINE and EMBASE were searched and literature comparing change in FEV1 in COPD patients taking ICS-containing medications with patients taking non-ICS-containing medications were identified. Titles, abstract, and full texts were screened and information extracted using the PICO checklist. Risk of bias was assessed using the Cochrane Risk of Bias tool and a descriptive synthesis of the literature was carried out due to high heterogeneity of included studies.Seventeen studies met our inclusion criteria. We found that the difference in change in FEV1 in people using ICS and non-ICS containing medications depended on the study follow-up time. Shorter follow-up studies (1 year or less) were more likely to report an increase in FEV1 from baseline in both patients on ICS and in patients on non-ICS-containing medications, with the majority of these studies showing a greater increase in FEV1 in patients on ICS-containing medications. Longer follow-up studies (greater than 1 year) were more likely to report a decline in FEV1 from baseline in patients on ICS and in patients on non-ICS containing medications but rates of FEV1 decline were similar.Further studies are needed to better understand changes in FEV1 when ICS-containing medications are prescribed and to determine whether ICS-containing medications influence rate of decline in FEV1 in the long term. Results from inclusive trials and observational patient cohorts may provide information more generalisable to a population of COPD patients.

Blood-based systems biology biomarkers for next-generation clinical trials in Alzheimer's disease
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Alzheimer's disease (AD)-a complex disease showing multiple pathomechanistic alterations-is triggered by nonlinear dynamic interactions of genetic/epigenetic and environmental risk factors, which, ultimately, converge into a biologically heterogeneous disease. To tackle the burden of AD during early preclinical stages, accessible blood-based biomarkers are currently being developed. Specifically, next-generation clinical trials are expected to integrate positive and negative predictive blood-based biomarkers into study designs to evaluate, at the individual level, target druggability and potential drug resistance mechanisms. In this scenario, systems biology holds promise to accelerate validation and qualification for clinical trial contexts of use-including proof-of-mechanism, patient selection, assessment of treatment efficacy and safety rates, and prognostic evaluation. Albeit in their infancy, systems biology-based approaches are poised to identify relevant AD "signatures" through multifactorial and interindividual variability, allowing us to decipher disease pathophysiology and etiology. Hopefully, innovative biomarker-drug codevelopment strategies will be the road ahead towards effective disease-modifying drugs.
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La Enfermedad de Alzheimer (EA) es una enfermedad compleja que presenta múltiples alteraciones patomecánicas, que se desencadena por interacciones dinámicas no lineales de factores de riesgo genéticos / epigenéticos y ambientales, los que, en definitiva, convergen en una enfermedad biológicamente heterogénea. Para hacer frente a la carga de la EA durante las etapas preclínicas tempranas, actualmente se están desarrollando biomarcadores sanguíneos de fácil accesibilidad. Específicamente, se espera que los ensayos clínicos de próxima generación integren biomarcadores sanguíneos predictivos tanto positivos como negativos en los diseños de los estudios para evaluar, a nivel individual, la capacidad de la droga objetivo y los posibles mecanismos de resistencia a los medicamentos. En este contexto, la biología de sistemas promete acelerar la validación y la calificación de su empleo en los ensayos clínicos, incluida la prueba del mecanismo, la selección de pacientes, la evaluación de la eficacia del tratamiento y los porcentajes de seguridad, y la evaluación pronóstica. A pesar de estar en sus comienzos, los enfoques basados en la biología de sistemas están preparados para identificar "firmas" de EA relevantes a través de la variabilidad multifactorial e interindividual, lo que nos permite descifrar la fisiopatología y la etiología de la enfermedad. Ojalá, las estrategias innovadoras conjuntas del desarrollo de biomarcadores y de medicamentos sean el camino adecuado para conseguir fármacos eficaces que modifiquen la enfermedad.

La maladie d'Alzheimer (MA) ­ maladie complexe présentant des altérations nombreuses pathomécaniques ­ est déclenchée par des interactions dynamiques non linéaires entre des facteurs de risques génétiques et épigénétiques et environnementaux qui, au bout du compte, aboutissent à une maladie biologiquement hétérogène. Pour réduire la charge de morbidité de la MA durant ses premiers stades précliniques, des biomarqueurs sanguins sont actuellement développés. Spécifiquement, la prochaine génération d'essais cliniques devrait intégrer ces biomarqueurs sanguins positifs ou négatifs prédictifs de la maladie dans des études qui auront pour but d'évaluer, à un niveau individuel, des cibles pouvant être traitées par des candidats médicaments et de potentiels mécanismes de résistance à ces médicaments. Dans ce contexte, la biologie des systèmes devrait permettre d'accélérer la validation et la qualification de leur utilisation dans les études cliniques ­ incluant la preuve du mécanisme d'action, la sélection des patients, la confirmation de l'efficacité du traitement et son niveau de sécurité, ainsi que l'évaluation pronostique. Bien que nous en soyons au tout début, les approches reposant sur la biologie des systèmes sont sur le point d'identifier des « signatures ¼ pertinentes de la MA grâce à des variables multifactorielles et interindividuelles, qui nous permettront d'élucider la pathophysiologie et l'étiologie de la maladie. Avec un peu de chance, les stratégies innovantes de codéveloppement de biomarqueurs et de médicaments nous mèneront vers des médicaments efficaces pour lutter contre la maladie.

Inhaled corticosteroids, blood eosinophils, and FEV1 decline in patients with COPD in a large UK primary health care setting.

Background: Inhaled corticosteroid (ICS)-containing medications slow rate of decline of FEV1. Blood eosinophil (EOS) levels are associated with the degree of exacerbation reduction with ICS. Purpose: We investigated whether FEV1 decline differs between patients with and without ICS, stratified by blood EOS level. Patients and methods: The UK Clinical Practice Research Datalink (primary care records) and Hospital Episode Statistics (hospital records) were used to identify COPD patients aged 35 years or older, who were current or ex-smokers with ≥2 FEV1 measurements ≥6 months apart. Prevalent ICS use and the nearest EOS count to start of follow-up were identified. Patients were classified at baseline as higher stratum EOS (≥150 cell/µL) on ICS; higher stratum EOS not on ICS; lower stratum EOS (<150 cells/µL) on ICS; and lower stratum EOS not on ICS. In addition, an incident ICS cohort was used to investigate the rate of FEV1 change by EOS and incident ICS use. Mixed-effects linear regression was used to compare rates of FEV1 change in mL/year. Results: A total of 26,675 COPD patients met our inclusion criteria (median age 69, 46% female). The median duration of follow up was 4.2 years. The rate of FEV1 change in prevalent ICS users was slower than non-ICS users (-12.6 mL/year vs -21.1 mL/year; P =0.001). The rate of FEV1 change was not significantly different when stratified by EOS level. The rate of FEV1 change in incident ICS users increased (+4.2 mL/year) vs -21.2 mL/year loss in non-ICS users; P<0.001. In patients with high EOS, incident ICS patients showed an increase in FEV1 (+12 mL/year) compared to non-ICS users whose FEV1 decreased (-20.8 mL/year); P<0.001. No statistical difference was seen in low EOS patients. Incident ICS use is associated with an improvement in FEV1 change, however, over time this association is lost. Conclusion: Regardless of blood EOS level, prevalent ICS use is associated with slower rates of FEV1 decline in COPD.

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer's disease risk.

Alzheimer's disease (AD) is highly heritable and recent studies have identified over 20 disease-associated genomic loci. Yet these only explain a small proportion of the genetic variance, indicating that undiscovered loci remain. Here, we performed a large genome-wide association study of clinically diagnosed AD and AD-by-proxy (71,880 cases, 383,378 controls). AD-by-proxy, based on parental diagnoses, showed strong genetic correlation with AD (rg = 0.81). Meta-analysis identified 29 risk loci, implicating 215 potential causative genes. Associated genes are strongly expressed in immune-related tissues and cell types (spleen, liver, and microglia). Gene-set analyses indicate biological mechanisms involved in lipid-related processes and degradation of amyloid precursor proteins. We show strong genetic correlations with multiple health-related outcomes, and Mendelian randomization results suggest a protective effect of cognitive ability on AD risk. These results are a step forward in identifying the genetic factors that contribute to AD risk and add novel insights into the neurobiology of AD.

Blood-based biomarkers for Alzheimer disease: mapping the road to the clinic.

Biomarker discovery and development for clinical research, diagnostics and therapy monitoring in clinical trials have advanced rapidly in key areas of medicine - most notably, oncology and cardiovascular diseases - allowing rapid early detection and supporting the evolution of biomarker-guided, precision-medicine-based targeted therapies. In Alzheimer disease (AD), breakthroughs in biomarker identification and validation include cerebrospinal fluid and PET markers of amyloid-ß and tau proteins, which are highly accurate in detecting the presence of AD-associated pathophysiological and neuropathological changes. However, the high cost, insufficient accessibility and/or invasiveness of these assays limit their use as viable first-line tools for detecting patterns of pathophysiology. Therefore, a multistage, tiered approach is needed, prioritizing development of an initial screen to exclude from these tests the high numbers of people with cognitive deficits who do not demonstrate evidence of underlying AD pathophysiology. This Review summarizes the efforts of an international working group that aimed to survey the current landscape of blood-based AD biomarkers and outlines operational steps for an effective academic-industry co-development pathway from identification and assay development to validation for clinical use.

A Blood Test for Alzheimer's Disease: Progress, Challenges, and Recommendations.

Ever since the discovery of APOEɛ4 around 25 years ago, researchers have been excited about the potential of a blood test for Alzheimer's disease (AD). Since then researchers have looked for genetic, protein, metabolite, and/or gene expression markers of AD and related phenotypes. However, no blood test for AD is yet being used in the clinical setting. We first review the trends and challenges in AD blood biomarker research, before giving our personal recommendations to help researchers overcome these challenges. While some degree of consistency and replication has been seen across independent studies, several high-profile studies have seemingly failed to replicate. Partly due to academic incentives, there is a reluctance in the field to report predictive ability, to publish negative findings, and to independently replicate the work of others. If this can be addressed, then we will know sooner whether a blood test for AD or related phenotypes with clinical utility can be developed.

Plasma Protein Biomarkers for the Prediction of CSF Amyloid and Tau and [18F]-Flutemetamol PET Scan Result.

Background: Blood biomarkers may aid in recruitment to clinical trials of Alzheimer's disease (AD) modifying therapeutics by triaging potential trials participants for amyloid positron emission tomography (PET) or cerebrospinal fluid (CSF) Aß and tau tests. Objective: To discover a plasma proteomic signature associated with CSF and PET measures of AD pathology. Methods: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) based proteomics were performed in plasma from participants with subjective cognitive decline (SCD), mild cognitive impairment (MCI), and AD, recruited to the Amsterdam Dementia Cohort, stratified by CSF Tau/Aß42 (n = 50). Technical replication and independent validation were performed by immunoassay in plasma from SCD, MCI, and AD participants recruited to the Amsterdam Dementia Cohort with CSF measures (n = 100), MCI participants enrolled in the GE067-005 study with [18F]-Flutemetamol PET amyloid measures (n = 173), and AD, MCI and cognitively healthy participants from the EMIF 500 study with CSF Aß42 measurements (n = 494). Results: 25 discovery proteins were nominally associated with CSF Tau/Aß42 (P < 0.05) with associations of ficolin-2 (FCN2), apolipoprotein C-IV and fibrinogen ß chain confirmed by immunoassay (P < 0.05). In the GE067-005 cohort, FCN2 was nominally associated with PET amyloid (P < 0.05) replicating the association with CSF Tau/Aß42. There were nominally significant associations of complement component 3 with PET amyloid, and apolipoprotein(a), apolipoprotein A-I, ceruloplasmin, and PPY with MCI conversion to AD (all P < 0.05). In the EMIF 500 cohort FCN2 was trending toward a significant relationship with CSF Aß42 (P ≈ 0.05), while both A1AT and clusterin were nominally significantly associated with CSF Aß42 (both P < 0.05). Conclusion: Associations of plasma proteins with multiple measures of AD pathology and progression are demonstrated. To our knowledge this is the first study to report an association of FCN2 with AD pathology. Further testing of the proteins in larger independent cohorts will be important.

Genetic Risk as a Marker of Amyloid-ß and Tau Burden in Cerebrospinal Fluid.

BACKGROUND: The search for a biomarker of Alzheimer's disease (AD) pathology (amyloid-ß (Aß) and tau) is ongoing, with the best markers currently being measurements of Aß and tau in cerebrospinal fluid (CSF) and via positron emission tomography (PET) scanning. These methods are relatively invasive, costly, and often have high screening failure rates. Consequently, research is aiming to elucidate blood biomarkers of Aß and tau. OBJECTIVE: This study aims to investigate a case/control polygenic risk score (PGRS) as a marker of tau and investigate blood markers of a combined Aß and tau outcome for the first time. A sub-study also considers plasma tau as markers of Aß and tau pathology in CSF. METHODS: We used data from the EDAR*, DESCRIPA**, and Alzheimer's Disease Neuroimaging Initiative (ADNI) cohorts in a logistic regression analysis to investigate blood markers of Aß and tau in CSF. In particular, we investigated the extent to which a case/control PGRS is predictive of CSF tau, CSF amyloid, and a combined amyloid and tau outcome. The predictive ability of models was compared to that of age, gender, and APOE genotype ('basic model'). RESULTS: In EDAR and DESCRIPA test data, inclusion of a case/control PGRS was no more predictive of Aß, and a combined Aß and tau endpoint than the basic models (accuracies of 66.0%, and 73.3% respectively). The tau model saw a small increase in accuracy compared to basic models (59.6%). ADNI 2 test data also showed a slight increase in accuracy for the Aß model when compared to the basic models (61.4%). CONCLUSION: We see some evidence that a case/control PGRS is marginally more predictive of Aß and tau pathology than the basic models. The search for predictive factors of Aß and tau pathologies, above and beyond demographic information, is still ongoing. Better understanding of AD risk alleles, development of more sensitive assays, and studies of larger sample size are three avenues that may provide such factors. However, the clinical utility of possible predictors of brain Aß and tau pathologies must also be investigated.*'Beta amyloid oligomers in the early diagnosis of AD and as marker for treatment response'**'Development of screening guidelines and criteria for pre-dementia Alzheimer's disease'.