45 results on '"Kiddle, Steven J."'
Search Results
2. Graph Neural Networks with Adaptive Readouts
- Author
-
Buterez, David, Janet, Jon Paul, Kiddle, Steven J., Oglic, Dino, and Liò, Pietro
- Subjects
Computer Science - Machine Learning ,Computer Science - Artificial Intelligence - Abstract
An effective aggregation of node features into a graph-level representation via readout functions is an essential step in numerous learning tasks involving graph neural networks. Typically, readouts are simple and non-adaptive functions designed such that the resulting hypothesis space is permutation invariant. Prior work on deep sets indicates that such readouts might require complex node embeddings that can be difficult to learn via standard neighborhood aggregation schemes. Motivated by this, we investigate the potential of adaptive readouts given by neural networks that do not necessarily give rise to permutation invariant hypothesis spaces. We argue that in some problems such as binding affinity prediction where molecules are typically presented in a canonical form it might be possible to relax the constraints on permutation invariance of the hypothesis space and learn a more effective model of the affinity by employing an adaptive readout function. Our empirical results demonstrate the effectiveness of neural readouts on more than 40 datasets spanning different domains and graph characteristics. Moreover, we observe a consistent improvement over standard readouts (i.e., sum, max, and mean) relative to the number of neighborhood aggregation iterations and different convolutional operators., Comment: Published at NeurIPS 2022. 10 pages, 5 figures, 1 table
- Published
- 2022
3. Modelling local and general quantum mechanical properties with attention-based pooling
- Author
-
Buterez, David, Janet, Jon Paul, Kiddle, Steven J., Oglic, Dino, and Liò, Pietro
- Published
- 2023
- Full Text
- View/download PDF
4. Blood-based systems biology biomarkers for next-generation clinical trials in Alzheimer's disease .
- Author
-
Hampel, Harald, Vergallo, Andrea, Afshar, Mohammad, Akman-Anderson, Leyla, Arenas, Joaquín, Benda, Norbert, Batrla, Richard, Broich, Karl, Caraci, Filippo, Cuello, A Claudio, Emanuele, Enzo, Haberkamp, Marion, Kiddle, Steven J, Lucía, Alejandro, Mapstone, Mark, Verdooner, Steven R, Woodcock, Janet, and Lista, Simone
- Subjects
Humans ,Alzheimer Disease ,Early Diagnosis ,Eligibility Determination ,Clinical Trials as Topic ,Biomarkers ,Precision Medicine ,Drug Development ,Alzheimer’s disease ,biomarker-drug codevelopment ,blood-based biomarker ,clinical trial ,context of use ,pathophysiology ,precision medicine ,predictive biomarker ,systems biology ,Alzheimer's disease ,Clinical Research ,Clinical Trials and Supportive Activities ,Aging ,Acquired Cognitive Impairment ,Brain Disorders ,Alzheimer's Disease ,Prevention ,Alzheimer's Disease including Alzheimer's Disease Related Dementias ,Neurodegenerative ,Dementia ,Neurosciences ,4.1 Discovery and preclinical testing of markers and technologies ,5.1 Pharmaceuticals ,Other Medical and Health Sciences ,Psychiatry - Abstract
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. .
- Published
- 2019
5. Urate‐lowering therapy in patients with hyperuricemia and heart failure: A retrospective cohort study using the UK Clinical Practice Research Datalink.
- Author
-
Kiddle, Steven J., Sundell, Karolina Andersson, Perl, Shira, Nolan, Stephen, and Bjursell, Magnus
- Subjects
HEART failure patients ,MEDICAL research ,PROPORTIONAL hazards models ,COHORT analysis ,HOSPITAL statistics - Abstract
Background: Elevated serum uric acid (sUA) is associated with heart failure (HF). Hypothesis: Urate‐lowering therapy (ULT) in HF is associated with lower risk of HF hospitalization (hHF) and mortality. Methods: Data on patients with HF and gout or hyperuricemia in the Clinical Practice Research Datalink database linked to the Hospital Episode Statistics and the Office for National Statistics in the United Kingdom were analyzed. Risks of hHF and all‐cause mortality or cardiovascular‐related mortality by ULT exposure (ULT initiated within ≤6 months of gout or hyperuricemia diagnosis) were analyzed in a propensity score‐matched cohort using adjusted Cox proportional hazards regression models. Results: Of 2174 propensity score‐matched pairs, patients were predominantly male, aged >70 years, with mean ± standard deviation sUA 9.3 ± 1.8 (ULT‐exposed) and 9.4 ± 1.9 mg/dL (ULT‐unexposed). At 5 years, ULT‐exposed patients had a 43% lower risk of hHF or all‐cause mortality (adjusted hazard ratio [HR]: 0.57; 95% confidence interval [CI]: 0.51–0.65) and a 19% lower risk of hHF or cardiovascular‐related mortality (adjusted HR: 0.81; 95% CI: 0.71–0.92) versus no ULT exposure. Conclusion: ULT was associated with reduced risk of adverse clinical outcomes in patients with HF and gout or hyperuricemia over 5 years. Practitioner points: Raised serum uric acid is strongly associated with heart failure (HF); however, it is unknown whether urate‐lowering therapy (ULT) could help patients with HF.We assessed the relationship between ULT and HF outcomes using UK patient data, and found that the risk of the composite of hospital admission for HF or death was lower with ULT than with no ULT.These results support further investigation into the potential benefit of ULT in HF. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
6. Blood protein predictors of brain amyloid for enrichment in clinical trials?
- Author
-
Ashton, Nicholas J, Kiddle, Steven J, Graf, John, Ward, Malcolm, Baird, Alison L, Hye, Abdul, Westwood, Sarah, Wong, Karyuan Vivian, Dobson, Richard J, Rabinovici, Gil D, Miller, Bruce L, Rosen, Howard J, Torres, Andrew, Zhang, Zhanpan, Thurfjell, Lennart, Covin, Antonia, Hehir, Cristina Tan, Baker, David, Bazenet, Chantal, Lovestone, Simon, and AIBL Research Group
- Subjects
AIBL Research Group ,Alzheimer's disease ,Biomarker ,Clinical trials ,Fibrinogen γ-chain ,Plasma ,Proteomics ,β amyloid ,Clinical Trials and Supportive Activities ,Brain Disorders ,Prevention ,Dementia ,Neurosciences ,Aging ,Alzheimer's Disease ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Neurodegenerative ,Acquired Cognitive Impairment ,Clinical Research ,4.1 Discovery and preclinical testing of markers and technologies ,Neurological ,Genetics - Abstract
BackgroundMeasures of neocortical amyloid burden (NAB) identify individuals who are at substantially greater risk of developing Alzheimer's disease (AD). Blood-based biomarkers predicting NAB would have great utility for the enrichment of AD clinical trials, including large-scale prevention trials.MethodsNontargeted proteomic discovery was applied to 78 subjects from the Australian Imaging, Biomarkers and Lifestyle Flagship Study of Ageing with a range of NAB values. Technical and independent replications were performed by immunoassay.ResultsSeventeen discovery candidates were selected for technical replication. α2-Macroglobulin, fibrinogen γ-chain (FGG), and complement factor H-related protein 1 were confirmed to be associated with NAB. In an independent cohort, FGG plasma levels combined with age predicted NAB had a sensitivity of 59% and specificity of 78%.ConclusionA single blood protein, FGG, combined with age, was shown to relate to NAB and therefore could have potential for enrichment of clinical trial populations.
- Published
- 2015
7. Evaluating clinical outcomes and prognosis in patients with cirrhosis and portal hypertension: a retrospective observational cohort study
- Author
-
Lee, Nerissa Hoi Ching, primary, Kiddle, Steven J, additional, Chandankhede, Shardul, additional, Agrawal, Shubh, additional, Bean, Daniel M, additional, Hunt, Phillip R, additional, Parker, Victoria E R, additional, Greasley, Peter J, additional, and Ambery, Philip, additional
- Published
- 2023
- Full Text
- View/download PDF
8. Using systems biology approaches to elucidate gene regulatory networks controlling the plant defence response
- Author
-
Kiddle, Steven J.
- Subjects
570 ,QK Botany - Abstract
Transcriptional regulation controlling pathogen-responsive gene expression in Arabidopsis is believed to underlie the plant defence response, which confers partial immunity of Arabidopsis to infection by Botrytis cinerea. In this thesis networks of transcriptional regulation mediating the defence response are studied in various ways. First transcriptional regulation was predicted for all genes differentially expressed during B. cinerea infection by development of a novel clustering approach, Temporal Clustering by Affinity Propagation (TCAP). This approach finds groups of genes whose expression profile time series have strong time-delayed correlation, a measure that is demonstrated to be more predictive of transcriptional regulation than conventionally used similarity measures. TCAP predicts the known regulation of GI by LHY, and co-clusters ORA59 and some of its downstream targets. Predicted novel regulators of pathogen-responsive gene expression were then studied in a reverse genetics screen, which discovered several novel but weakly altered susceptibility phenotypes. Comparison of predicted targets to known targets was complicated by the sparsity of mutant versus wildtype gene expression experiments performed during B. cinerea infections in the literature. To explore the context-dependence of transcriptional regulation, evidence of transcriptional regulation in different contexts was collected. This was compiled to generate a qualitative model of transcriptional regulation during the defence response. This model was validated and extended by experimental analysis of transcription factor-promoter binding in Yeast and transcriptional activation in planta. Comparative transcriptomics showed that downstream genes of some of these regulators | TGA3, ARF2, ERF1 and ANAC072 | are over-represented in the list of genes differentially expressed during B. cinerea infection, which is consistent with these targets being regulated by them during B. cinerea infection. Finally this qualitative model was used as prior information and was used along with gene expression time series to infer quantitative models of the gene regulatory network mediating the defence response. Some known regulation was predicted, and additionally ANAC055 was predicted to be a central regulator of pathogenresponsive gene expression.
- Published
- 2012
9. Inhaled corticosteroids and FEV1 decline in chronic obstructive pulmonary disease: a systematic review
- Author
-
Whittaker, Hannah R., Jarvis, Debbie, Sheikh, Mohamed R., Kiddle, Steven J., and Quint, Jennifer K.
- Published
- 2019
- Full Text
- View/download PDF
10. Blood-based biomarkers for Alzheimer disease: mapping the road to the clinic
- Author
-
Hampel, Harald, O’Bryant, Sid E., Molinuevo, José L., Zetterberg, Henrik, Masters, Colin L., Lista, Simone, Kiddle, Steven J., Batrla, Richard, and Blennow, Kaj
- Published
- 2018
- Full Text
- View/download PDF
11. Blood protein predictors of brain amyloid for enrichment in clinical trials?
- Author
-
Ashton, Nicholas J., Kiddle, Steven J., Graf, John, Ward, Malcolm, Baird, Alison L., Hye, Abdul, Westwood, Sarah, Wong, Karyuan Vivian, Dobson, Richard J., Rabinovici, Gil D., Miller, Bruce L., Rosen, Howard J., Torres, Andrew, Zhang, Zhanpan, Thurfjell, Lennart, Covin, Antonia, Hehir, Cristina Tan, Baker, David, Bazenet, Chantal, and Lovestone, Simon
- Published
- 2015
- Full Text
- View/download PDF
12. Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis
- Author
-
Windram, Oliver, Madhou, Priyadharshini, McHattie, Stuart, Hill, Claire, Hickman, Richard, Cooke, Emma, Jenkins, Dafyd J., Penfold, Christopher A., Baxter, Laura, Breeze, Emily, Kiddle, Steven J., Rhodes, Johanna, Atwell, Susanna, Kliebenstein, Daniel J., Kim, Youn-sung, Stegle, Oliver, Borgwardt, Karsten, Zhang, Cunjin, Tabrett, Alex, Legaie, Roxane, Moore, Jonathan, Finkenstadt, Bärbel, Wild, David L., Mead, Andrew, Rand, David, Beynon, Jim, Ott, Sascha, Buchanan-Wollaston, Vicky, and Denby, Katherine J.
- Published
- 2012
13. Characteristics Associated with Accelerated Lung Function Decline in a Primary Care Population with Chronic Obstructive Pulmonary Disease
- Author
-
Whittaker, Hannah R, Pimenta, Jeanne M, Jarvis, Deborah, Kiddle, Steven J, Quint, Jennifer K, and GlaxoSmithKline Services Unlimited
- Subjects
chronic obstructive ,Primary Health Care ,Respiratory System ,spirometry ,Vital Capacity ,lung function ,International Journal of Chronic Obstructive Pulmonary Disease ,respiratory system ,respiratory tract diseases ,Respiratory Function Tests ,Pulmonary Disease, Chronic Obstructive ,Forced Expiratory Volume ,Humans ,Female ,1102 Cardiorespiratory Medicine and Haematology ,Lung ,circulatory and respiratory physiology ,Original Research ,pulmonary disease ,Aged - Abstract
Hannah R Whittaker,1 Jeanne M Pimenta,2 Deborah Jarvis,1 Steven J Kiddle,3 Jennifer K Quint1 1Respiratory Epidemiology, Occupational Medicine and Public Health, National Heart and Lung Institute, Imperial College London, London, UK; 2Epidemiology (Value Evidence and Outcomes), GlaxoSmithKline, R&D, Uxbridge, UK; 3MRC Biostatistics Unit, University of Cambridge, Cambridge, UKCorrespondence: Hannah R WhittakerImperial College, Emmanuel Kaye Building, National Heart and Lung Institute, London, UKEmail h.whittaker@imperial.ac.ukBackground: 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.Keywords: pulmonary disease, chronic obstructive, spirometry, lung function
- Published
- 2020
14. Evaluating clinical outcomes and prognosis in patients with cirrhosis and portal hypertension: a retrospective observational cohort study.
- Author
-
Nerissa Hoi Ching Lee, Kiddle, Steven J., Chandankhede, Shardul, Agrawal, Shubh, Bean, Daniel M., Hunt, Phillip R., Parker, Victoria E. R., Greasley, Peter J., and Ambery, Philip
- Published
- 2023
- Full Text
- View/download PDF
15. Challenges and Pitfalls of Using Repeat Spirometry Recordings in Routine Primary Care Data to Measure FEV1 Decline in a COPD Population
- Author
-
Whittaker, Hannah R, primary, Kiddle, Steven J, additional, and Quint, Jennifer K, additional
- Published
- 2021
- Full Text
- View/download PDF
16. MiRNA-15b and miRNA-125b are associated with regional Aβ-PET and FDG-PET uptake in cognitively normal individuals with subjective memory complaints
- Author
-
Vergallo, Andrea, Lista, Simone, group, INSIGHT-preAD study, Lucía, Alejandro, Mango, Dalila, Mapstone, Mark, Neri, Christian, Nisticò, Robert, O'Bryant, Sid E, Palermo, Giovanni, Perry, George, Ritchie, Craig, Rossi, Simone, Initiative, Alzheimer Precision Medicine, Saidi, Amira, Santarnecchi, Emiliano, Schneider, Lon S, Sporns, Olaf, Toschi, Nicola, Valenzuela, Pedro L, Vellas, Bruno, Verdooner, Steven R, Villain, Nicolas, Giudici, Kelly Virecoulon, Bakardjian, Hovagim, Watling, Mark, Welikovitch, Lindsay A, Woodcock, Janet, Younesi, Erfan, Zugaza, José L, Benali, Habib, Bertin, Hugo, Bonheur, Joel, Boukadida, Laurie, Boukerrou, Nadia, Cavedo, Enrica, Chiesa, Patrizia, Zhao, Yuhai, Colliot, Olivier, Dubois, Bruno, Dubois, Marion, Epelbaum, Stéphane, Gagliardi, Geoffroy, Genthon, Remy, Habert, Marie-Odile, Hampel, Harald, Houot, Marion, Kas, Aurélie, Lemercier, Pablo, Lamari, Foudil, Levy, Marcel, Metzinger, Christiane, Mochel, Fanny, Nyasse, Francis, Poisson, Catherine, Potier, Marie-Claude, Revillon, Marie, Santos, Antonio, Teipel, Stefan J, Andrade, Katia Santos, Sole, Marine, Surtee, Mohmed, de Schotten, Michel Thiebaut, Younsi, Nadjia, Afshar, Mohammad, Aguilar, Lisi Flores, Akman-Anderson, Leyla, Arenas, Joaquín, Ávila, Jesús, Babiloni, Claudio, Baldacci, Filippo, Batrla, Richard, Benda, Norbert, Black, Keith L, Bokde, Arun L W, Bonuccelli, Ubaldo, Broich, Karl, Cacciola, Francesco, Caraci, Filippo, Caruso, Giuseppe, Castrillo, Juan, Ceravolo, Roberto, Chiesa, Patrizia A, Corbo, Massimo, Corvol, Jean-Christophe, Cuello, Augusto Claudio, Cummings, Jeffrey L, Depypere, Herman, Duggento, Andrea, Emanuele, Enzo, Escott-Price, Valentina, Federoff, Howard, Ferretti, Maria Teresa, Fiandaca, Massimo, Frank, Richard A, Garaci, Francesco, Lukiw, Walter J, Geerts, Hugo, Giacobini, Ezio, Giorgi, Filippo S, Goetzl, Edward J, Graziani, Manuela, Haberkamp, Marion, Hänisch, Britta, Herholz, Karl, Hernandez, Felix, Imbimbo, Bruno P, Kapogiannis, Dimitrios, Karran, Eric, Kiddle, Steven J, Kim, Seung H, Koronyo, Yosef, Koronyo-Hamaoui, Maya, Langevin, Todd, Lehéricy, Stéphane, Llavero, Francisco, Lorenceau, Jean, Ministre de l'Enseignement Supérieur, de la Recherche et de l'Innovation (France), Sorbonne Université, AXA Research Fund, Fondation partenariale, Fondation pour la Recherche sur Alzheimer, Investissement d’Avenir French program, Vergallo, Andrea [0000-0002-0208-6384], Apollo - University of Cambridge Repository, Alzheimer Precision Medicine [CHU Pitié-Salpétriêre] (GRC 21 AMP), CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de la Mémoire et de la Maladie d'Alzheimer [Paris] (IM2A), Sorbonne Université (SU), Service de Neurologie [CHU Pitié-Salpêtrière], IFR70-CHU Pitié-Salpêtrière [AP-HP], Louisiana State University (LSU), University of Rostock, Laboratoire d'Imagerie Biomédicale (LIB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), CATI Multicenter Neuroimaging Platform (CATI), Service de médecine nucléaire [CHU Pitié-Salpétrière], Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Department of Psychiatry, Psychosomatic Medicine and Psychotherapy [Goethe Universität], Goethe-Universität Frankfurt am Main, HAL-SU, Gestionnaire, Alzheimer Precision Medicine [CHU Pitié-Salpétriêre] (GRC 21 APM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de la Mémoire et de la Maladie d'Alzheimer [CHU Pitié-Salpétriêre] (IM2A), Service de Médecine nucléaire [CHU Pitié-Salpétrière], Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France, Groupe de recherche clinique Alzheimer Precision Medicine (GRC 21 - APM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Laboratoire d'Imagerie Biomédicale [Paris] (LIB), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Service de neurologie 1 [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)
- Subjects
Apolipoprotein E ,Aging ,[SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,Disease ,miRNAs plasma concentrations ,Alzheimer's Disease ,amyloid-β (Aβ)-positron emission tomography (Aβ-PET) ,Prognostic markers ,0302 clinical medicine ,Medicine ,Psychology ,Aetiology ,education.field_of_study ,MicroARNs ,Settore FIS/07 ,amyloid ,Brain ,Pathophysiology ,ALZHEIMERS-DISEASE ,Psychiatry and Mental health ,Alzheimer's disease (AD) ,Public Health and Health Services ,[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,MiRNA ,medicine.medical_specialty ,18F-fluorodeoxyglucose-PET (18F-FDG-PET) ,BIOMARKERS ,Neurociencias ,Clinical Sciences ,Molecular neuroscience ,Predictive markers ,Article ,VESICLES ,lcsh:RC321-571 ,03 medical and health sciences ,Memory ,Clinical Research ,Alzheimer Disease ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,microRNA ,Genetics ,Humans ,education ,Biological Psychiatry ,Prevention ,Memory, MiRNA, Alzheimer, biological markers, amyloid ,030104 developmental biology ,Endocrinology ,Cross-Sectional Studies ,Positron-Emission Tomography ,CELLS ,Dementia ,diagnostic imaging [Alzheimer Disease] ,INSIGHT-preAD study group ,030217 neurology & neurosurgery ,[SDV.NEU.SC] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences ,0301 basic medicine ,genetics [Alzheimer Disease] ,Pilot Projects ,Neurodegenerative ,Medicine and Health Sciences ,2.1 Biological and endogenous factors ,genetics [MicroRNAs] ,MIR-125B ,screening and diagnosis ,PLASMA ,[SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences ,Detection ,Real-time polymerase chain reaction ,Neurological ,medicine.symptom ,biological markers ,Biotechnology ,EXPRESSION ,Population ,metabolism [Amyloid beta-Peptides] ,Asymptomatic ,Salud mental ,Cellular and Molecular Neuroscience ,ADULT ,Fluorodeoxyglucose F18 ,Internal medicine ,Acquired Cognitive Impairment ,ddc:610 ,Allele ,lcsh:Neurosciences. Biological psychiatry. Neuropsychiatry ,diagnostic imaging [Brain] ,Psiquiatría ,Amyloid beta-Peptides ,Enfermedad de alzheimer ,business.industry ,[SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,Neurosciences ,Alzheimer Precision Medicine Initiative ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Brain Disorders ,4.1 Discovery and preclinical testing of markers and technologies ,MicroRNAs ,metabolism [Brain] ,Alzheimer ,business ,Psychiatric disorders - Abstract
There is substantial experimental evidence for dysregulation of several microRNA (miRNA) expression levels in Alzheimer’s disease (AD). MiRNAs modulate critical brain intracellular signaling pathways and are associated with AD core pathophysiological mechanisms. First, we conducted a real-time quantitative PCR-based pilot study to identify a set of brain-enriched miRNAs in a monocentric cohort of cognitively normal individuals with subjective memory complaints, a condition associated with increased risk of AD. Second, we investigated the impact of age, sex, and the Apolipoprotein E ε4 (APOE ε4) allele, on the identified miRNA plasma concentrations. In addition, we explored the cross-sectional and longitudinal association of the miRNAs plasma concentrations with regional brain metabolic uptake using amyloid-β (Aβ)-positron emission tomography (Aβ-PET) and F-fluorodeoxyglucose-PET (F-FDG-PET). We identified a set of six brain-enriched miRNAs—miRNA-125b, miRNA-146a, miRNA-15b, miRNA-148a, miRNA-26b, and miRNA-100. Age, sex, and APOE ε4 allele were not associated with individual miRNA abundance. MiRNA-15b concentrations were significantly lower in the Aβ-PET-positive compared to Aβ-PET-negative individuals. Furthermore, we found a positive effect of the miRNA-15b*time interaction on regional metabolic F-FDG-PET uptake in the left hippocampus. Plasma miRNA-125b concentrations, as well as the miRNA-125b*time interaction (over a 2-year follow-up), were negatively associated with regional Aβ-PET standard uptake value ratio in the right anterior cingulate cortex. At baseline, we found a significantly negative association between plasma miRNA-125b concentrations and F-FDG-PET uptake in specific brain regions. In an asymptomatic at-risk population for AD, we show significant associations between plasma concentrations of miRNA-125b and miRNA-15b with core neuroimaging biomarkers of AD pathophysiology. Our results, coupled with existing experimental evidence, suggest a potential protective anti-Aβ effect of miRNA-15b and a biological link between miRNA-125b and Aβ-independent neurotoxic pathways., “Investissement d’Avenir” (ANR-10-AIHU-06) French program. The study was promoted in collaboration with the “CHU de Bordeaux” (coordination CIC EC7), the promoter of Memento cohort, funded by the Foundation Plan-Alzheimer. The study was further supported by AVID/Lilly. CATI is a French neuroimaging platform funded by the French Plan Alzheimer (available at http://cati-neuroimaging.com). A.V. is an employee of Eisai Inc. This work has been performed during his previous position at Sorbonne University, Paris, France. H.H. is an employee of Eisai Inc. This work has been performed during his previous position at Sorbonne University, Paris, France. At Sorbonne University he was supported by the AXA Research Fund, the “Fondation partenariale Sorbonne Université” and the “Fondation pour la Recherche sur Alzheimer
- Published
- 2021
17. Challenges and Pitfalls of Using Repeat Spirometry Recordings in Routine Primary Care Data to Measure FEV1 Decline in a COPD Population
- Author
-
Whittaker,Hannah R, Kiddle,Steven J, Quint,Jennifer K, Whittaker,Hannah R, Kiddle,Steven J, and Quint,Jennifer K
- Abstract
Hannah R Whittaker,1 Steven J Kiddle,2 Jennifer K Quint1 1National Heart and Lung Institute, Imperial College London, London, UK; 2MRC Biostatistics Unit, University of Cambridge, Cambridge, UKCorrespondence: Hannah R Whittaker Email h.whittaker@imperial.ac.ukBackground: 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 â 18.7mL/year (95% CI â 19.2 to â 18.2) to â 16.5mL/year (95% CI â 17.3 to â 15.7). Rates of FEV1 decline in populations that excluded patients with potential measurement error ranged from â 79.4mL/year (95% CI â 80.7 to â 78.2) to â 46.8mL/year (95% CI â 47.6 to
- Published
- 2021
18. Wigwams: identifying gene modules co-regulated across multiple biological conditions
- Author
-
Polanski, Krzysztof, Rhodes, Johanna, Hill, Claire, Zhang, Peijun, Jenkins, Dafyd J., Kiddle, Steven J., Jironkin, Aleksey, Beynon, Jim, Buchanan-Wollaston, Vicky, Ott, Sascha, and Denby, Katherine J.
- Published
- 2014
- Full Text
- View/download PDF
19. Author Correction: Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk (Nature Genetics, (2019), 51, 3, (404-413), 10.1038/s41588-018-0311-9)
- Author
-
Jansen, Iris E., Savage, Jeanne E., Watanabe, Kyoko, Bryois, Julien, Williams, Dylan M., Steinberg, Stacy, Sealock, Julia, Karlsson, Ida K., Hägg, Sara, Athanasiu, Lavinia, Voyle, Nicola, Proitsi, Petroula, Witoelar, Aree, Stringer, Sven, Aarsland, Dag, Almdahl, Ina S., Andersen, Fred, Bergh, Sverre, Bettella, Francesco, Bjornsson, Sigurbjorn, Brækhus, Anne, Bråthen, Geir, de Leeuw, Christiaan, Desikan, Rahul S., Djurovic, Srdjan, Dumitrescu, Logan, Fladby, Tormod, Hohman, Timothy J., Jonsson, Palmi V., Kiddle, Steven J., Rongve, Arvid, Saltvedt, Ingvild, Sando, Sigrid B., Selbæk, Geir, Shoai, Maryam, Skene, Nathan G., Snaedal, Jon, Stordal, Eystein, Ulstein, Ingun D., Wang, Yunpeng, White, Linda R., Hardy, John, Hjerling-Leffler, Jens, Sullivan, Patrick F., van der Flier, Wiesje M., Dobson, Richard, Davis, Lea K., Stefansson, Hreinn, Stefansson, Kari, Pedersen, Nancy L., Ripke, Stephan, Andreassen, Ole A., Posthuma, Danielle, Neurology, Amsterdam Reproduction & Development (AR&D), Amsterdam Neuroscience - Complex Trait Genetics, Human genetics, APH - Personalized Medicine, and APH - Methodology
- Abstract
In the version of this article initially published, in the phase 3 meta-analysis, the UK Biobank results were overweighed with a slightly larger (5%) N, thus resulting in a minimal underestimation of effect sizes and in P values marginally less significant than their actual values. Because the differences were on the order of the ninth decimal, there is no notable effect on the results or the conclusions drawn. The summary statistics have been updated accordingly at https://ctg.cncr.nl/software/summary_statistics. The Data availability statement has been updated to include the new URL in the HTML and PDF versions of the article.
- Published
- 2020
20. Characteristics Associated with Accelerated Lung Function Decline in a Primary Care Population with Chronic Obstructive Pulmonary Disease
- Author
-
Whittaker,Hannah R, Pimenta,Jeanne M, Jarvis,Deborah, Kiddle,Steven J, Quint,Jennifer K, Whittaker,Hannah R, Pimenta,Jeanne M, Jarvis,Deborah, Kiddle,Steven J, and Quint,Jennifer K
- Abstract
Hannah R Whittaker,1 Jeanne M Pimenta,2 Deborah Jarvis,1 Steven J Kiddle,3 Jennifer K Quint1 1Respiratory Epidemiology, Occupational Medicine and Public Health, National Heart and Lung Institute, Imperial College London, London, UK; 2Epidemiology (Value Evidence and Outcomes), GlaxoSmithKline, R&D, Uxbridge, UK; 3MRC Biostatistics Unit, University of Cambridge, Cambridge, UKCorrespondence: Hannah R WhittakerImperial College, Emmanuel Kaye Building, National Heart and Lung Institute, London, UKEmail h.whittaker@imperial.ac.ukBackground: 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 w
- Published
- 2020
21. Accelerated FEV1decline and risk of cardiovascular disease and mortality in a primary care population of COPD patients
- Author
-
Whittaker, Hannah R., primary, Bloom, Chloe, additional, Morgan, Ann, additional, Jarvis, Deborah, additional, Kiddle, Steven J., additional, and Quint, Jennifer K., additional
- Published
- 2020
- Full Text
- View/download PDF
22. Prediction of five-year mortality after COPD diagnosis using primary care records
- Author
-
Kiddle, Steven J., primary, Whittaker, Hannah R., additional, Seaman, Shaun R., additional, and Quint, Jennifer K., additional
- Published
- 2020
- Full Text
- View/download PDF
23. Dysregulated Antibody, Natural Killer Cell and Immune Mediator Profiles in Autoimmune Thyroid Diseases
- Author
-
Martin, Tiphaine C., primary, Ilieva, Kristina M., additional, Visconti, Alessia, additional, Beaumont, Michelle, additional, Kiddle, Steven J., additional, Dobson, Richard J. B., additional, Mangino, Massimo, additional, Lim, Ee Mun, additional, Pezer, Marija, additional, Steves, Claire J., additional, Bell, Jordana T., additional, Wilson, Scott G., additional, Lauc, Gordan, additional, Roederer, Mario, additional, Walsh, John P., additional, Spector, Tim D., additional, and Karagiannis, Sophia N., additional
- Published
- 2020
- Full Text
- View/download PDF
24. Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana
- Author
-
Kiddle, Steven J., Windram, Oliver P., McHattie, Stuart, Mead, Andrew, Beynon, Jim, Buchanan-Wollaston, Vicky, Denby, Katherine J., and Mukherjee, Sach
- Published
- 2010
25. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer's disease risk
- Author
-
Jansen, Iris E, Savage, Jeanne E, Watanabe, Kyoko, Bryois, Julien, Williams, Dylan M, Steinberg, Stacy, Sealock, Julia, Karlsson, Ida K, Hägg, Sara, Athanasiu, Lavinia, Voyle, Nicola, Proitsi, Petroula, Witoelar, Aree, Stringer, Sven, Aarsland, Dag, Almdahl, Ina S, Andersen, Fred, Bergh, Sverre, Bettella, Francesco, Bjornsson, Sigurbjorn, Brækhus, Anne, Bråthen, Geir, de Leeuw, Christiaan, Desikan, Rahul S, Djurovic, Srdjan, Dumitrescu, Logan, Fladby, Tormod, Hohman, Timothy J, Jonsson, Palmi V, Kiddle, Steven J, Rongve, Arvid, Saltvedt, Ingvild, Sando, Sigrid B, Selbæk, Geir, Shoai, Maryam, Skene, Nathan G, Snaedal, Jon, Stordal, Eystein, Ulstein, Ingun D, Wang, Yunpeng, White, Linda R, Hardy, John, Hjerling-Leffler, Jens, Sullivan, Patrick F, van der Flier, Wiesje M, Dobson, Richard, Davis, Lea K, Stefansson, Hreinn, Stefansson, Kari, Pedersen, Nancy L, Ripke, Stephan, Andreassen, Ole A, Posthuma, Danielle, Jansen, Iris E, Savage, Jeanne E, Watanabe, Kyoko, Bryois, Julien, Williams, Dylan M, Steinberg, Stacy, Sealock, Julia, Karlsson, Ida K, Hägg, Sara, Athanasiu, Lavinia, Voyle, Nicola, Proitsi, Petroula, Witoelar, Aree, Stringer, Sven, Aarsland, Dag, Almdahl, Ina S, Andersen, Fred, Bergh, Sverre, Bettella, Francesco, Bjornsson, Sigurbjorn, Brækhus, Anne, Bråthen, Geir, de Leeuw, Christiaan, Desikan, Rahul S, Djurovic, Srdjan, Dumitrescu, Logan, Fladby, Tormod, Hohman, Timothy J, Jonsson, Palmi V, Kiddle, Steven J, Rongve, Arvid, Saltvedt, Ingvild, Sando, Sigrid B, Selbæk, Geir, Shoai, Maryam, Skene, Nathan G, Snaedal, Jon, Stordal, Eystein, Ulstein, Ingun D, Wang, Yunpeng, White, Linda R, Hardy, John, Hjerling-Leffler, Jens, Sullivan, Patrick F, van der Flier, Wiesje M, Dobson, Richard, Davis, Lea K, Stefansson, Hreinn, Stefansson, Kari, Pedersen, Nancy L, Ripke, Stephan, Andreassen, Ole A, and Posthuma, Danielle
- Abstract
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.
- Published
- 2019
- Full Text
- View/download PDF
26. Inhaled corticosteroids, blood eosinophils, and FEV1 decline in patients with COPD in a large UK primary health care setting
- Author
-
Whittaker,Hannah R, Müllerova,Hana, Jarvis,Deborah, Barnes,Neil C, Jones,Paul W, Compton,Chris H, Kiddle,Steven J, Quint,Jennifer K, Whittaker,Hannah R, Müllerova,Hana, Jarvis,Deborah, Barnes,Neil C, Jones,Paul W, Compton,Chris H, Kiddle,Steven J, and Quint,Jennifer K
- Abstract
Hannah R Whittaker,1 Hana Müllerova,2 Deborah Jarvis,1 Neil C Barnes,2 Paul W Jones,2 Chris H Compton,2 Steven J Kiddle,3 Jennifer K Quint11National Heart and Lung Institute, Imperial College London, London, UK; 2Respiratory Epidemiology, GlaxoSmithKline R&D, Uxbridge, UK; 3MRC Biostatistics Unit, University of Cambridge, Cambridge, UKBackground: 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, inci
- Published
- 2019
27. Challenges and Pitfalls of Using Repeat Spirometry Recordings in Routine Primary Care Data to Measure FEV1 Decline in a COPD Population.
- Author
-
Whittaker, Hannah R, Kiddle, Steven J, and Quint, Jennifer K
- Subjects
- *
CHRONIC obstructive pulmonary disease , *MEASUREMENT errors , *FORCED expiratory volume , *PRIMARY care , *SPIROMETRY - Abstract
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. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
28. Alzheimer's disease: are blood and brain markers related? A systematic review
- Author
-
Khan, Ali T, Dobson, Richard JB, Sattlecker, Martina, Kiddle, Steven J, Kiddle, Steven [0000-0003-4350-7437], and Apollo - University of Cambridge Repository
- Subjects
Aging ,Biomedical ,FOS: Clinical medicine ,Neurosciences ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Neurodegenerative ,Alzheimer's Disease ,Brain Disorders ,4.1 Discovery and preclinical testing of markers and technologies ,Clinical Medicine and Science ,Neurological ,Acquired Cognitive Impairment ,Dementia ,1109 Neurosciences ,Research Articles ,Research Article - Abstract
Objective Peripheral protein biomarkers of Alzheimer's disease (AD) may help identify novel treatment avenues by allowing early diagnosis, recruitment to clinical trials, and treatment initiation. The purpose of this review was to determine which proteins have been found to be differentially expressed in the AD brain and whether these proteins are also found within the blood of AD patients. Methods A two‐stage approach was conducted. The first stage involved conducting a systematic search to identify discovery‐based brain proteomic studies of AD. The second stage involved comparing whether proteins found to be differentially expressed in AD brain were also differentially expressed in the blood. Results Across 11 discovery based brain proteomic studies 371 proteins were at different levels in the AD brain. Nine proteins were frequently found, defined as appearing in at least three separate studies. Of these proteins heat‐shock cognate 71 kDa, ubiquitin carboxyl‐terminal hydrolase isozyme L1, and 2′,3′‐cyclic nucleotide 3′ phosphodiesterase alone were found to share a consistent direction of change, being consistently upregulated in studies they appeared in. Eighteen proteins seen as being differentially expressed within the AD brain were present in blood proteomic studies of AD. Only complement C4a was seen multiple times within both the blood and brain proteomic studies. Interpretation We report a number of proteins appearing in both the blood and brain of AD patients. Of these proteins, C4a may be a good candidate for further follow‐up in large‐scale replication efforts.
- Published
- 2016
29. Inhaled corticosteroids, blood eosinophils, and FEV1 decline in patients with COPD in a large UK primary health care setting
- Author
-
Whittaker, Hannah R, primary, Müllerova, Hana, additional, Jarvis, Deborah, additional, Barnes, Neil C, additional, Jones, Paul W, additional, Compton, Chris H, additional, Kiddle, Steven J, additional, and Quint, Jennifer K, additional
- Published
- 2019
- Full Text
- View/download PDF
30. Plasma Protein Biomarkers for the Prediction of CSF Amyloid and Tau and [18F]-Flutemetamol PET Scan Result
- Author
-
Westwood, Sarah, primary, Baird, Alison L., additional, Hye, Abdul, additional, Ashton, Nicholas J., additional, Nevado-Holgado, Alejo J., additional, Anand, Sneha N., additional, Liu, Benjamine, additional, Newby, Danielle, additional, Bazenet, Chantal, additional, Kiddle, Steven J., additional, Ward, Malcolm, additional, Newton, Ben, additional, Desai, Keyur, additional, Tan Hehir, Cristina, additional, Zanette, Michelle, additional, Galimberti, Daniela, additional, Parnetti, Lucilla, additional, Lleó, Alberto, additional, Baker, Susan, additional, Narayan, Vaibhav A., additional, van der Flier, Wiesje M., additional, Scheltens, Philip, additional, Teunissen, Charlotte E., additional, Visser, Pieter Jelle, additional, and Lovestone, Simon, additional
- Published
- 2018
- Full Text
- View/download PDF
31. Inhaled corticosteroids, blood eosinophils, and FEV1 decline in patients with COPD in a large UK primary health care setting.
- Author
-
Whittaker, Hannah R, Müllerova, Hana, Jarvis, Deborah, Barnes, Neil C, Jones, Paul W, Compton, Chris H, Kiddle, Steven J, and Quint, Jennifer K
- Published
- 2019
- Full Text
- View/download PDF
32. Blood-based systems biology biomarkers fornext-generation clinical trials in Alzheimer’s disease
- Author
-
Hampel, Harald, Vergallo, Andrea, Afshar, Mohammad, Akman-Anderson, Leyla, Arenas, Joaquín, Benda, Norbert, Batrla, Richard, Broich, Karl, Caraci, Filippo, Cuello, A. Claudio, Emanuele, Enzo, Haberkamp, Marion, Kiddle, Steven J., Lucía, Alejandro, Mapstone, Mark, Verdooner, Steven R., Woodcock, Janet, and Lista, Simone
- Abstract
Alzheimer’s disease (AD)—a complex disease showing multiple pathomechanisticalterations—is triggered by nonlinear dynamic interactions of genetic/epigeneticand environmental risk factors, which, ultimately, converge into a biologicallyheterogeneous disease. To tackle the burden of AD during early preclinicalstages, accessible blood-based biomarkers are currently being developed.Specifically, next-generation clinical trials are expected to integrate positiveand negative predictive blood-based biomarkers into study designs to evaluate,at the individual level, target druggability and potential drug resistancemechanisms. In this scenario, systems biology holds promise to acceleratevalidation and qualification for clinical trial contexts of use—includingproof-of-mechanism, patient selection, assessment of treatment efficacy andsafety rates, and prognostic evaluation. Albeit in their infancy, systemsbiology-based approaches are poised to identify relevant AD “signatures” throughmultifactorial and interindividual variability, allowing us to decipher diseasepathophysiology and etiology. Hopefully, innovative biomarker-drug codevelopmentstrategies will be the road ahead towards effective disease-modifyingdrugs.
- Published
- 2019
- Full Text
- View/download PDF
33. Wigwams: identifying gene modules co-regulated across multiple biological conditions
- Author
-
Polanski, Krzysztof, primary, Rhodes, Johanna, additional, Hill, Claire, additional, Zhang, Peijun, additional, Jenkins, Dafyd J., additional, Kiddle, Steven J., additional, Jironkin, Aleksey, additional, Beynon, Jim, additional, Buchanan-Wollaston, Vicky, additional, Ott, Sascha, additional, and Denby, Katherine J., additional
- Published
- 2013
- Full Text
- View/download PDF
34. Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana
- Author
-
Kiddle, Steven J., primary, Windram, Oliver P. F., additional, McHattie, Stuart, additional, Mead, Andrew, additional, Beynon, Jim, additional, Buchanan-Wollaston, Vicky, additional, Denby, Katherine J., additional, and Mukherjee, Sach, additional
- Published
- 2009
- Full Text
- View/download PDF
35. A Subset of Cerebrospinal Fluid Proteins from a Multi-Analyte Panel Associated with Brain Atrophy, Disease Classification and Prediction in Alzheimer’s Disease.
- Author
-
Khan, Wasim, Aguilar, Carlos, Kiddle, Steven J., Doyle, Orla, Thambisetty, Madhav, Muehlboeck, Sebastian, Sattlecker, Martina, Newhouse, Stephen, Lovestone, Simon, Dobson, Richard, Giampietro, Vincent, Westman, Eric, Simmons, Andrew, and null, null
- Subjects
CEREBROSPINAL fluid proteins ,CEREBRAL atrophy ,ALZHEIMER'S disease ,BRAIN imaging ,MAGNETIC resonance imaging - Abstract
In this exploratory neuroimaging-proteomic study, we aimed to identify CSF proteins associated with AD and test their prognostic ability for disease classification and MCI to AD conversion prediction. Our study sample consisted of 295 subjects with CSF multi-analyte panel data and MRI at baseline downloaded from ADNI. Firstly, we tested the statistical effects of CSF proteins (n = 83) to measures of brain atrophy, CSF biomarkers, ApoE genotype and cognitive decline. We found that several proteins (primarily CgA and FABP) were related to either brain atrophy or CSF biomarkers. In relation to ApoE genotype, a unique biochemical profile characterised by low CSF levels of Apo E was evident in ε4 carriers compared to ε3 carriers. In an exploratory analysis, 3/83 proteins (SGOT, MCP-1, IL6r) were also found to be mildly associated with cognitive decline in MCI subjects over a 4-year period. Future studies are warranted to establish the validity of these proteins as prognostic factors for cognitive decline. For disease classification, a subset of proteins (n = 24) combined with MRI measurements and CSF biomarkers achieved an accuracy of 95.1% (Sensitivity 87.7%; Specificity 94.3%; AUC 0.95) and accurately detected 94.1% of MCI subjects progressing to AD at 12 months. The subset of proteins included FABP, CgA, MMP-2, and PPP as strong predictors in the model. Our findings suggest that the marker of panel of proteins identified here may be important candidates for improving the earlier detection of AD. Further targeted proteomic and longitudinal studies would be required to validate these findings with more generalisability. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
36. Inhaled corticosteroids and FEV1 decline in chronic obstructive pulmonary disease: a systematic review.
- Author
-
Whittaker, Hannah R., Jarvis, Debbie, Sheikh, Mohamed R., Kiddle, Steven J., and Quint, Jennifer K.
- Subjects
OBSTRUCTIVE lung diseases ,META-analysis - Abstract
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. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
37. Using systems biology approaches to elucidate gene regulatory networks controlling the plant defence response
- Author
-
Kiddle, Steven J.
- Subjects
QK - Abstract
Transcriptional regulation controlling pathogen-responsive gene expression in Arabidopsis\ud is believed to underlie the plant defence response, which confers partial\ud immunity of Arabidopsis to infection by Botrytis cinerea. In this thesis networks\ud of transcriptional regulation mediating the defence response are studied in various\ud ways.\ud First transcriptional regulation was predicted for all genes differentially expressed\ud during B. cinerea infection by development of a novel clustering approach, Temporal\ud Clustering by Affinity Propagation (TCAP). This approach finds groups of\ud genes whose expression profile time series have strong time-delayed correlation, a\ud measure that is demonstrated to be more predictive of transcriptional regulation\ud than conventionally used similarity measures. TCAP predicts the known regulation\ud of GI by LHY, and co-clusters ORA59 and some of its downstream targets.\ud Predicted novel regulators of pathogen-responsive gene expression were then studied\ud in a reverse genetics screen, which discovered several novel but weakly altered\ud susceptibility phenotypes. Comparison of predicted targets to known targets was\ud complicated by the sparsity of mutant versus wildtype gene expression experiments\ud performed during B. cinerea infections in the literature.\ud To explore the context-dependence of transcriptional regulation, evidence of transcriptional\ud regulation in different contexts was collected. This was compiled to generate\ud a qualitative model of transcriptional regulation during the defence response.\ud This model was validated and extended by experimental analysis of transcription\ud factor-promoter binding in Yeast and transcriptional activation in planta. Comparative\ud transcriptomics showed that downstream genes of some of these regulators\ud | TGA3, ARF2, ERF1 and ANAC072 | are over-represented in the list of genes\ud differentially expressed during B. cinerea infection, which is consistent with these\ud targets being regulated by them during B. cinerea infection.\ud Finally this qualitative model was used as prior information and was used along\ud with gene expression time series to infer quantitative models of the gene regulatory\ud network mediating the defence response. Some known regulation was predicted,\ud and additionally ANAC055 was predicted to be a central regulator of pathogenresponsive\ud gene expression.
38. Circulating Proteomic Signatures of Chronological Age
- Author
-
Menni, Cristina, Kiddle, Steven J., Mangino, Massimo, Viñuela, Ana, Psatha, Maria, Steves, Claire, Sattlecker, Martina, Buil, Alfonso, Newhouse, Stephen, Nelson, Sally, Williams, Stephen, Voyle, Nicola, Soininen, Hilkka, Kloszewska, Iwona, Mecocci, Patrizia, Tsolaki, Magda, Vellas, Bruno, Lovestone, Simon, Spector, Tim D., Dobson, Richard, Valdes, Ana M., Menni, Cristina, Kiddle, Steven J., Mangino, Massimo, Viñuela, Ana, Psatha, Maria, Steves, Claire, Sattlecker, Martina, Buil, Alfonso, Newhouse, Stephen, Nelson, Sally, Williams, Stephen, Voyle, Nicola, Soininen, Hilkka, Kloszewska, Iwona, Mecocci, Patrizia, Tsolaki, Magda, Vellas, Bruno, Lovestone, Simon, Spector, Tim D., Dobson, Richard, and Valdes, Ana M.
- Abstract
To elucidate the proteomic features of aging in plasma, the subproteome targeted by the SOMAscan assay was profiled in blood samples from 202 females from the TwinsUK cohort. Findings were replicated in 677 independent individuals from the AddNeuroMed, Alzheimer's Research UK, and Dementia Case Registry cohorts. Results were further validated using RNAseq data from whole blood in TwinsUK and the most significant proteins were tested for association with aging-related phenotypes after adjustment for age. Eleven proteins were associated with chronological age and were replicated at protein level in an independent population. These were further investigated at gene expression level in 384 females from the TwinsUK cohort. The two most strongly associated proteins were chordin-like protein 1 (meta-analysis β [SE] = 0.013 [0.001], p = 3.66 × 10−46) and pleiotrophin (0.012 [0.005], p = 3.88 × 10−41). Chordin-like protein 1 was also significantly correlated with birthweight (0.06 [0.02], p = 0.005) and with the individual Framingham 10-years cardiovascular risk scores in TwinsUK (0.71 [0.18], p = 9.9 × 10−5). Pleiotrophin is a secreted growth factor with a plethora of functions in multiple tissues and known to be a marker for cardiovascular risk and osteoporosis. Our study highlights the importance of proteomics to identify some molecular mechanisms involved in human health and aging
39. Prediction of five-year mortality after COPD diagnosis using primary care records
- Author
-
Hannah R Whittaker, Steven J. Kiddle, Jennifer K Quint, Shaun R. Seaman, Kiddle, Steven J [0000-0003-4350-7437], Apollo - University of Cambridge Repository, and Kiddle, Steven J. [0000-0003-4350-7437]
- Subjects
Pulmonology ,Physiology ,Biochemistry ,Severity of Illness Index ,Geographical locations ,Body Mass Index ,Pulmonary Disease, Chronic Obstructive ,0302 clinical medicine ,Mathematical and Statistical Techniques ,Risk Factors ,Forced Expiratory Volume ,Medicine ,030212 general & internal medicine ,COPD ,Multidisciplinary ,Statistics ,Age Factors ,Middle Aged ,C-Reactive Proteins ,Prognosis ,Europe ,Survival Rate ,Physical sciences ,Physiological Parameters ,England ,Female ,Risk assessment ,Research Article ,Adult ,medicine.medical_specialty ,General Science & Technology ,Chronic Obstructive Pulmonary Disease ,Science ,MEDLINE ,Cardiology ,FOS: Physical sciences ,Context (language use) ,Primary care ,Risk Assessment ,03 medical and health sciences ,Diagnostic Medicine ,Severity of illness ,Humans ,European Union ,Statistical Methods ,Survival rate ,Aged ,Heart Failure ,Medicine and health sciences ,Primary Health Care ,Biology and life sciences ,business.industry ,Body Weight ,Proteins ,medicine.disease ,United Kingdom ,Asthma ,Research and analysis methods ,030228 respiratory system ,Emergency medicine ,People and places ,business ,Body mass index ,Mathematics ,Forecasting - Abstract
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/).
- Published
- 2020
- Full Text
- View/download PDF
40. Challenges and Pitfalls of Using Repeat Spirometry Recordings in Routine Primary Care Data to Measure FEV1 Decline in a COPD Population
- Author
-
Hannah R Whittaker, Steven J. Kiddle, Jennifer K Quint, Kiddle, Steven J [0000-0003-4350-7437], Quint, Jennifer K [0000-0003-0149-4869], and Apollo - University of Cambridge Repository
- Subjects
Spirometry ,Pediatrics ,medicine.medical_specialty ,media_common.quotation_subject ,Population ,spirometry ,Pulmonary disease ,Primary care ,Medicine, General & Internal ,electronic healthcare records ,General & Internal Medicine ,LUNG-FUNCTION DECLINE ,Linear regression ,Epidemiology ,medicine ,COPD ,education ,Pragmatic and Observational Research ,Original Research ,media_common ,Selection bias ,education.field_of_study ,Science & Technology ,medicine.diagnostic_test ,business.industry ,1103 Clinical Sciences ,lung function ,medicine.disease ,respiratory tract diseases ,business ,Life Sciences & Biomedicine - Abstract
Hannah R Whittaker,1 Steven J Kiddle,2 Jennifer K Quint1 1National Heart and Lung Institute, Imperial College London, London, UK; 2MRC Biostatistics Unit, University of Cambridge, Cambridge, UKCorrespondence: Hannah R Whittaker Email h.whittaker@imperial.ac.ukBackground: 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 â 18.7mL/year (95% CI â 19.2 to â 18.2) to â 16.5mL/year (95% CI â 17.3 to â 15.7). Rates of FEV1 decline in populations that excluded patients with potential measurement error ranged from â 79.4mL/year (95% CI â 80.7 to â 78.2) to â 46.8mL/year (95% CI â 47.6 to â 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.Keywords: electronic healthcare records, spirometry, COPD, lung function
- Published
- 2021
- Full Text
- View/download PDF
41. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk
- Author
-
Julia Sealock, Linda R. White, John Hardy, Geir Bråthen, Danielle Posthuma, Christiaan de Leeuw, Ingvild Saltvedt, Julien Bryois, Lea K. Davis, Timothy J. Hohman, Logan Dumitrescu, Nancy L. Pedersen, Petroula Proitsi, Francesco Bettella, Eystein Stordal, Dylan M. Williams, Sigrid Botne Sando, Sven Stringer, Stacy Steinberg, Jon Snaedal, Steven J. Kiddle, Jens Hjerling-Leffler, Fred Andersen, Ida K. Karlsson, Yunpeng Wang, Palmi V. Jonsson, Nicola Voyle, Jeanne E. Savage, Ingun Ulstein, Stephan Ripke, Richard Dobson, Anne Brækhus, Arvid Rongve, Sverre Bergh, Hreinn Stefansson, Dag Aarsland, Kyoko Watanabe, Patrick F. Sullivan, Maryam Shoai, Geir Selbæk, Sigurbjorn Bjornsson, Rahul S. Desikan, Srdjan Djurovic, Ina S. Almdahl, Sara Hägg, Kari Stefansson, Lavinia Athanasiu, Nathan G. Skene, Aree Witoelar, Iris E. Jansen, Ole A. Andreassen, Wiesje M. van der Flier, Tormod Fladby, Neurology, Amsterdam Neuroscience - Neurodegeneration, APH - Personalized Medicine, APH - Methodology, Epidemiology and Data Science, Human genetics, Amsterdam Reproduction & Development (AR&D), Complex Trait Genetics, Theoretical Computer Science, Functional Genomics, Jansen, Iris E [0000-0003-1901-8131], Savage, Jeanne E [0000-0002-2034-8341], Steinberg, Stacy [0000-0001-7726-5152], Hägg, Sara [0000-0002-2452-1500], Proitsi, Petroula [0000-0002-2553-6974], Stringer, Sven [0000-0003-3115-8532], Almdahl, Ina S [0000-0001-6070-4921], Bråthen, Geir [0000-0003-3224-7983], de Leeuw, Christiaan [0000-0003-1076-9828], Djurovic, Srdjan [0000-0002-8140-8061], Hohman, Timothy J [0000-0002-3377-7014], Kiddle, Steven J [0000-0003-4350-7437], Skene, Nathan G [0000-0002-6807-3180], Stordal, Eystein [0000-0002-2443-7923], Hjerling-Leffler, Jens [0000-0002-4539-1776], Dobson, Richard [0000-0003-4224-9245], Davis, Lea K [0000-0001-5143-2282], Stefansson, Kari [0000-0003-1676-864X], Andreassen, Ole A [0000-0002-4461-3568], Posthuma, Danielle [0000-0001-7582-2365], and Apollo - University of Cambridge Repository
- Subjects
MISSENSE MUTATIONS ,Male ,Genome-wide association study ,Disease ,VARIANTS ,ANNOTATION ,0302 clinical medicine ,RARE ,Polymorphism (computer science) ,POLYGENIC RISK ,11 Medical and Health Sciences ,GENE-EXPRESSION ,Genetics ,Genetics & Heredity ,0303 health sciences ,DEMENTIA ,VDP::Medical disciplines: 700::Clinical medical disciplines: 750::Geriatrics: 778 ,COGNITIVE RESERVE ,ASSOCIATION ,Middle Aged ,Female ,Alzheimer's disease ,Life Sciences & Biomedicine ,Adult ,Risk ,VDP::Medisinske Fag: 700::Basale medisinske, odontologiske og veterinærmedisinske fag: 710::Medisinsk genetikk: 714 ,Quantitative Trait Loci ,Biology ,Quantitative trait locus ,VDP::Medical disciplines: 700::Basic medical, dental and veterinary science disciplines: 710::Medical genetics: 714 ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,Young Adult ,SDG 3 - Good Health and Well-being ,Alzheimer Disease ,Genetic variation ,Mendelian randomization ,medicine ,Humans ,Genetic Predisposition to Disease ,030304 developmental biology ,Science & Technology ,Case-control study ,06 Biological Sciences ,medicine.disease ,DISCOVERY ,Case-Control Studies ,VDP::Medisinske Fag: 700::Klinisk medisinske fag: 750::Geriatri: 778 ,030217 neurology & neurosurgery ,Genome-Wide Association Study ,Developmental Biology - Abstract
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. © 2019. This is the authors' accepted and refereed manuscript to the chapter. The final authenticated version is available online at: http://dx.doi.org/10.1038/s41588-018-0311-9
- Published
- 2019
42. Challenges and Pitfalls of Using Repeat Spirometry Recordings in Routine Primary Care Data to Measure FEV 1 Decline in a COPD Population.
- Author
-
Whittaker HR, Kiddle SJ, and Quint JK
- Abstract
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 (FEV
1 ) 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., Competing Interests: HW reports grants from GSK, AZ, and BI, outside the submitted work; SK reports grants from Medical Research Council, during the conduct of the study; personal fees from Roche Diagnostics, personal fees from DIADEM, personal fees from AstraZeneca, outside the submitted work; JQ reports grants from British Lung Foundation and personal fees from AZ, Asthma UK, BI, Bayer, GSK, MRC, and Chiesi, outside the submitted work. The authors report no other conflicts of interest in this work., (© 2021 Whittaker et al.)- Published
- 2021
- Full Text
- View/download PDF
43. Accelerated FEV 1 decline and risk of cardiovascular disease and mortality in a primary care population of COPD patients.
- Author
-
Whittaker HR, Bloom C, Morgan A, Jarvis D, Kiddle SJ, and Quint JK
- Subjects
- Child, Child, Preschool, Disease Progression, Forced Expiratory Volume, Humans, Infant, Primary Health Care, Risk Factors, Brain Ischemia, Cardiovascular Diseases epidemiology, Pulmonary Disease, Chronic Obstructive complications, Stroke epidemiology
- Abstract
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 (FEV
1 ) 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., Competing Interests: Conflict of interest: H.R. Whittaker reports grants from GSK, AstraZeneca and BI, outside the submitted work. Conflict of interest: C. Bloom reports funding from AstraZeneca, Chiesi and Asthma UK, outside the submitted work. Conflict of interest: A. Morgan has nothing to disclose. Conflict of interest: D. Jarvis reports grants from the European Union and Cystic Fibrosis Trust, outside the submitted work. Conflict of interest: S.J. Kiddle reports grants from the Medical Research Council (grant number MR/P021573/1), during the conduct of the study; and personal fees from Roche Diagnostics and DIADEM, outside the submitted work. Conflict of interest: J.K. Quint reports grants from the British Lung Foundation, during the conduct of the study; grants and personal fees from AstraZeneca, BI, Bayer and GSK, and grants from Asthma UK, the Medical Research Council and Chiesi, outside the submitted work., (Copyright ©ERS 2021.)- Published
- 2021
- Full Text
- View/download PDF
44. Inhaled corticosteroids, blood eosinophils, and FEV 1 decline in patients with COPD in a large UK primary health care setting.
- Author
-
Whittaker HR, Müllerova H, Jarvis D, Barnes NC, Jones PW, Compton CH, Kiddle SJ, and Quint JK
- Subjects
- Administration, Inhalation, Aged, Aged, 80 and over, Disease Progression, Electronic Health Records, England, Female, Humans, Leukocyte Count, Lung physiopathology, Male, Middle Aged, Predictive Value of Tests, Pulmonary Disease, Chronic Obstructive blood, Pulmonary Disease, Chronic Obstructive diagnosis, Pulmonary Disease, Chronic Obstructive physiopathology, Risk Factors, Time Factors, Treatment Outcome, Adrenal Cortex Hormones administration & dosage, Eosinophils, Forced Expiratory Volume drug effects, Lung drug effects, Pulmonary Disease, Chronic Obstructive drug therapy
- Abstract
Background: Inhaled corticosteroid (ICS)-containing medications slow rate of decline of FEV
1 . 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., Competing Interests: Miss Whittaker reports grants from GlaxoSmithKline, during the conduct of the study; Dr Müllerova was employed by and reported personal fees from GlaxoSmithKline, during the conduct of the study; Dr Jarvis reports grants from European Union and Cystic Fibrosis Trust, outside the submitted work; she also reports grants from GlaxoSmithKline, during the conduct of the study. Dr Barnes is employed, holds shares and reports personal fees from GlaxoSmithKline, outside the submitted work; he also received grants from GlaxoSmithKline, during the conduct of the study. Dr Jones is employed by and reports personal fees from GlaxoSmithKline, during the conduct of the study; Dr Compton is employed, holds shares and reports personal fees from GlaxoSmithKline, during the conduct of the study; Dr Kiddle reports grants from MRC, during the conduct of the study; grants from Roche Diagnostics, Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council, National Institute for Health Research, Alzheimer’s Society, Eli Lily, and Jannsen, outside the submitted work; Dr Kiddle was supported by a MRC Career Development Award (MR/PO21573/1). Dr Quint reports grants from GlaxoSmithKline, during the conduct of the study; grants from The Health Foundation, MRC, Wellcome Trust, British Lung Foundation, Insmed, AstraZeneca, Bayer, Boehringer Ingelheim, Chiesi, Teva, and GlaxoSmithKline, outside the submitted work. The authors report no other conflicts of interest in this work.- Published
- 2019
- Full Text
- View/download PDF
45. Plasma Protein Biomarkers for the Prediction of CSF Amyloid and Tau and [ 18 F]-Flutemetamol PET Scan Result.
- Author
-
Westwood S, Baird AL, Hye A, Ashton NJ, Nevado-Holgado AJ, Anand SN, Liu B, Newby D, Bazenet C, Kiddle SJ, Ward M, Newton B, Desai K, Tan Hehir C, Zanette M, Galimberti D, Parnetti L, Lleó A, Baker S, Narayan VA, van der Flier WM, Scheltens P, Teunissen CE, Visser PJ, and Lovestone S
- Abstract
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) Aβ 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/Aβ
42 ( 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 [18 F]-Flutemetamol PET amyloid measures ( n = 173), and AD, MCI and cognitively healthy participants from the EMIF 500 study with CSF Aβ42 measurements ( n = 494). Results: 25 discovery proteins were nominally associated with CSF Tau/Aβ42 ( P < 0.05) with associations of ficolin-2 (FCN2), apolipoprotein C-IV and fibrinogen β 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/Aβ42 . 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 Aβ42 ( P ≈ 0.05), while both A1AT and clusterin were nominally significantly associated with CSF Aβ42 (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.- Published
- 2018
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.