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Jung W, Kim SE, Kim JP, Jang H, Park CJ, Kim HJ, Na DL, Seo SW, Suk HI. Deep learning model for individualized trajectory prediction of clinical outcomes in mild cognitive impairment. Front Aging Neurosci 2024; 16:1356745. [PMID: 38813529 PMCID: PMC11135285 DOI: 10.3389/fnagi.2024.1356745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 04/18/2024] [Indexed: 05/31/2024] Open
Abstract
Objectives Accurately predicting when patients with mild cognitive impairment (MCI) will progress to dementia is a formidable challenge. This work aims to develop a predictive deep learning model to accurately predict future cognitive decline and magnetic resonance imaging (MRI) marker changes over time at the individual level for patients with MCI. Methods We recruited 657 amnestic patients with MCI from the Samsung Medical Center who underwent cognitive tests, brain MRI scans, and amyloid-β (Aβ) positron emission tomography (PET) scans. We devised a novel deep learning architecture by leveraging an attention mechanism in a recurrent neural network. We trained a predictive model by inputting age, gender, education, apolipoprotein E genotype, neuropsychological test scores, and brain MRI and amyloid PET features. Cognitive outcomes and MRI features of an MCI subject were predicted using the proposed network. Results The proposed predictive model demonstrated good prediction performance (AUC = 0.814 ± 0.035) in five-fold cross-validation, along with reliable prediction in cognitive decline and MRI markers over time. Faster cognitive decline and brain atrophy in larger regions were forecasted in patients with Aβ (+) than with Aβ (-). Conclusion The proposed method provides effective and accurate means for predicting the progression of individuals within a specific period. This model could assist clinicians in identifying subjects at a higher risk of rapid cognitive decline by predicting future cognitive decline and MRI marker changes over time for patients with MCI. Future studies should validate and refine the proposed predictive model further to improve clinical decision-making.
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Affiliation(s)
- Wonsik Jung
- Department of Brain and Cognitive Engineering, Korea University, Seoul, Republic of Korea
| | - Si Eun Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Neurology, Inje University College of Medicine, Haeundae Paik Hospital, Busan, Republic of Korea
| | - Jun Pyo Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Neuroscience Center, Seoul, Republic of Korea
- Alzheimer’s Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
| | - Hyemin Jang
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chae Jung Park
- National Cancer Center Research Institute, Goyang, Republic of Korea
| | - Hee Jin Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Neuroscience Center, Seoul, Republic of Korea
- Alzheimer’s Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
| | - Duk L. Na
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Neuroscience Center, Seoul, Republic of Korea
- Alzheimer’s Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
| | - Sang Won Seo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Neuroscience Center, Seoul, Republic of Korea
- Alzheimer’s Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
- Center for Clinical Epidemiology, Samsung Medical Center, Seoul, Republic of Korea
- Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Heung-Il Suk
- Department of Artificial Intelligence, Korea University, Seoul, Republic of Korea
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Oh K, Yoon JS, Suk HI. Learn-Explain-Reinforce: Counterfactual Reasoning and its Guidance to Reinforce an Alzheimer's Disease Diagnosis Model. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2023; 45:4843-4857. [PMID: 35947563 DOI: 10.1109/tpami.2022.3197845] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Existing studies on disease diagnostic models focus either on diagnostic model learning for performance improvement or on the visual explanation of a trained diagnostic model. We propose a novel learn-explain-reinforce (LEAR) framework that unifies diagnostic model learning, visual explanation generation (explanation unit), and trained diagnostic model reinforcement (reinforcement unit) guided by the visual explanation. For the visual explanation, we generate a counterfactual map that transforms an input sample to be identified as an intended target label. For example, a counterfactual map can localize hypothetical abnormalities within a normal brain image that may cause it to be diagnosed with Alzheimer's disease (AD). We believe that the generated counterfactual maps represent data-driven knowledge about a target task, i.e., AD diagnosis using structural MRI, which can be a vital source of information to reinforce the generalization of the trained diagnostic model. To this end, we devise an attention-based feature refinement module with the guidance of the counterfactual maps. The explanation and reinforcement units are reciprocal and can be operated iteratively. Our proposed approach was validated via qualitative and quantitative analysis on the ADNI dataset. Its comprehensibility and fidelity were demonstrated through ablation studies and comparisons with existing methods.
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Prosser L, Macdougall A, Sudre CH, Manning EN, Malone IB, Walsh P, Goodkin O, Pemberton H, Barkhof F, Biessels GJ, Cash DM, Barnes J. Predicting Cognitive Decline in Older Adults Using Baseline Metrics of AD Pathologies, Cerebrovascular Disease, and Neurodegeneration. Neurology 2023; 100:e834-e845. [PMID: 36357185 PMCID: PMC9984210 DOI: 10.1212/wnl.0000000000201572] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/28/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Dementia is a growing socioeconomic challenge that requires early intervention. Identifying biomarkers that reliably predict clinical progression early in the disease process would better aid selection of individuals for future trial participation. Here, we compared the ability of baseline, single time-point biomarkers (CSF amyloid 1-42, CSF ptau-181, white matter hyperintensities (WMH), cerebral microbleeds, whole-brain volume, and hippocampal volume) to predict decline in cognitively normal individuals who later converted to mild cognitive impairment (MCI) (CNtoMCI) and those with MCI who later converted to an Alzheimer disease (AD) diagnosis (MCItoAD). METHODS Standardized baseline biomarker data from AD Neuroimaging Initiative 2 (ADNI2)/GO and longitudinal diagnostic data (including ADNI3) were used. Cox regression models assessed biomarkers in relation to time to change in clinical diagnosis using all follow-up time points available. Models were fit for biomarkers univariately and together in a multivariable model. Hazard ratios (HRs) were compared to evaluate biomarkers. Analyses were performed separately in CNtoMCI and MCItoAD groups. RESULTS For CNtoMCI (n = 189), there was strong evidence that higher WMH volume (individual model: HR 1.79, p = 0.002; fully adjusted model: HR 1.98, p = 0.003) and lower hippocampal volume (individual: HR 0.54, p = 0.001; fully adjusted: HR 0.40, p < 0.001) were associated with conversion to MCI individually and independently. For MCItoAD (n = 345), lower hippocampal (individual model: HR 0.45, p < 0.001; fully adjusted model: HR 0.55, p < 0.001) and whole-brain volume (individual: HR 0.31, p < 0.001; fully adjusted: HR 0.48, p = 0.02), increased CSF ptau (individual: HR 1.88, p < 0.001; fully adjusted: HR 1.61, p < 0.001), and lower CSF amyloid (individual: HR 0.37, p < 0.001; fully adjusted: HR 0.62, p = 0.008) were most strongly associated with conversion to AD individually and independently. DISCUSSION Lower hippocampal volume was a consistent predictor of clinical conversion to MCI and AD. CSF and brain volume biomarkers were predictive of conversion to AD from MCI, whereas WMH were predictive of conversion to MCI from cognitively normal. The predictive ability of WMH in the CNtoMCI group may be interpreted as some being on a different pathologic pathway, such as vascular cognitive impairment.
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Affiliation(s)
- Lloyd Prosser
- From the Department of Neurodegenerative Disease (L.P., A.M., C.H.S., E.N.M., I.B.M., P.W., H.P., D.M.C., J.B.), Dementia Research Centre, UCL Queen Square Institute of Neurology, London; Medical Statistics (A.M.), London School of Hygiene and Tropical Medicine; School of Biomedical Engineering and Imaging Sciences (C.H.S.), King's College London; Centre for Medical Image Computing (C.H.S., O.G., H.P., F.B.) and Department of Population Sciences and Experimental Medicine (C.H.S.), MRC Unit for Lifelong Health and Ageing at UCL, University College London, United Kingdom; Department of Radiology and Nuclear Medicine (F.B.), VU University Medical Center, Amsterdam Neuroscience; and Department of Neurology and Neurosurgery (G.J.B.), UMC Utrecht Brain Center, University Medical Center Utrecht, the Netherlands.
| | - Amy Macdougall
- From the Department of Neurodegenerative Disease (L.P., A.M., C.H.S., E.N.M., I.B.M., P.W., H.P., D.M.C., J.B.), Dementia Research Centre, UCL Queen Square Institute of Neurology, London; Medical Statistics (A.M.), London School of Hygiene and Tropical Medicine; School of Biomedical Engineering and Imaging Sciences (C.H.S.), King's College London; Centre for Medical Image Computing (C.H.S., O.G., H.P., F.B.) and Department of Population Sciences and Experimental Medicine (C.H.S.), MRC Unit for Lifelong Health and Ageing at UCL, University College London, United Kingdom; Department of Radiology and Nuclear Medicine (F.B.), VU University Medical Center, Amsterdam Neuroscience; and Department of Neurology and Neurosurgery (G.J.B.), UMC Utrecht Brain Center, University Medical Center Utrecht, the Netherlands
| | - Carole H Sudre
- From the Department of Neurodegenerative Disease (L.P., A.M., C.H.S., E.N.M., I.B.M., P.W., H.P., D.M.C., J.B.), Dementia Research Centre, UCL Queen Square Institute of Neurology, London; Medical Statistics (A.M.), London School of Hygiene and Tropical Medicine; School of Biomedical Engineering and Imaging Sciences (C.H.S.), King's College London; Centre for Medical Image Computing (C.H.S., O.G., H.P., F.B.) and Department of Population Sciences and Experimental Medicine (C.H.S.), MRC Unit for Lifelong Health and Ageing at UCL, University College London, United Kingdom; Department of Radiology and Nuclear Medicine (F.B.), VU University Medical Center, Amsterdam Neuroscience; and Department of Neurology and Neurosurgery (G.J.B.), UMC Utrecht Brain Center, University Medical Center Utrecht, the Netherlands
| | - Emily N Manning
- From the Department of Neurodegenerative Disease (L.P., A.M., C.H.S., E.N.M., I.B.M., P.W., H.P., D.M.C., J.B.), Dementia Research Centre, UCL Queen Square Institute of Neurology, London; Medical Statistics (A.M.), London School of Hygiene and Tropical Medicine; School of Biomedical Engineering and Imaging Sciences (C.H.S.), King's College London; Centre for Medical Image Computing (C.H.S., O.G., H.P., F.B.) and Department of Population Sciences and Experimental Medicine (C.H.S.), MRC Unit for Lifelong Health and Ageing at UCL, University College London, United Kingdom; Department of Radiology and Nuclear Medicine (F.B.), VU University Medical Center, Amsterdam Neuroscience; and Department of Neurology and Neurosurgery (G.J.B.), UMC Utrecht Brain Center, University Medical Center Utrecht, the Netherlands
| | - Ian B Malone
- From the Department of Neurodegenerative Disease (L.P., A.M., C.H.S., E.N.M., I.B.M., P.W., H.P., D.M.C., J.B.), Dementia Research Centre, UCL Queen Square Institute of Neurology, London; Medical Statistics (A.M.), London School of Hygiene and Tropical Medicine; School of Biomedical Engineering and Imaging Sciences (C.H.S.), King's College London; Centre for Medical Image Computing (C.H.S., O.G., H.P., F.B.) and Department of Population Sciences and Experimental Medicine (C.H.S.), MRC Unit for Lifelong Health and Ageing at UCL, University College London, United Kingdom; Department of Radiology and Nuclear Medicine (F.B.), VU University Medical Center, Amsterdam Neuroscience; and Department of Neurology and Neurosurgery (G.J.B.), UMC Utrecht Brain Center, University Medical Center Utrecht, the Netherlands
| | - Phoebe Walsh
- From the Department of Neurodegenerative Disease (L.P., A.M., C.H.S., E.N.M., I.B.M., P.W., H.P., D.M.C., J.B.), Dementia Research Centre, UCL Queen Square Institute of Neurology, London; Medical Statistics (A.M.), London School of Hygiene and Tropical Medicine; School of Biomedical Engineering and Imaging Sciences (C.H.S.), King's College London; Centre for Medical Image Computing (C.H.S., O.G., H.P., F.B.) and Department of Population Sciences and Experimental Medicine (C.H.S.), MRC Unit for Lifelong Health and Ageing at UCL, University College London, United Kingdom; Department of Radiology and Nuclear Medicine (F.B.), VU University Medical Center, Amsterdam Neuroscience; and Department of Neurology and Neurosurgery (G.J.B.), UMC Utrecht Brain Center, University Medical Center Utrecht, the Netherlands
| | - Olivia Goodkin
- From the Department of Neurodegenerative Disease (L.P., A.M., C.H.S., E.N.M., I.B.M., P.W., H.P., D.M.C., J.B.), Dementia Research Centre, UCL Queen Square Institute of Neurology, London; Medical Statistics (A.M.), London School of Hygiene and Tropical Medicine; School of Biomedical Engineering and Imaging Sciences (C.H.S.), King's College London; Centre for Medical Image Computing (C.H.S., O.G., H.P., F.B.) and Department of Population Sciences and Experimental Medicine (C.H.S.), MRC Unit for Lifelong Health and Ageing at UCL, University College London, United Kingdom; Department of Radiology and Nuclear Medicine (F.B.), VU University Medical Center, Amsterdam Neuroscience; and Department of Neurology and Neurosurgery (G.J.B.), UMC Utrecht Brain Center, University Medical Center Utrecht, the Netherlands
| | - Hugh Pemberton
- From the Department of Neurodegenerative Disease (L.P., A.M., C.H.S., E.N.M., I.B.M., P.W., H.P., D.M.C., J.B.), Dementia Research Centre, UCL Queen Square Institute of Neurology, London; Medical Statistics (A.M.), London School of Hygiene and Tropical Medicine; School of Biomedical Engineering and Imaging Sciences (C.H.S.), King's College London; Centre for Medical Image Computing (C.H.S., O.G., H.P., F.B.) and Department of Population Sciences and Experimental Medicine (C.H.S.), MRC Unit for Lifelong Health and Ageing at UCL, University College London, United Kingdom; Department of Radiology and Nuclear Medicine (F.B.), VU University Medical Center, Amsterdam Neuroscience; and Department of Neurology and Neurosurgery (G.J.B.), UMC Utrecht Brain Center, University Medical Center Utrecht, the Netherlands
| | - Frederik Barkhof
- From the Department of Neurodegenerative Disease (L.P., A.M., C.H.S., E.N.M., I.B.M., P.W., H.P., D.M.C., J.B.), Dementia Research Centre, UCL Queen Square Institute of Neurology, London; Medical Statistics (A.M.), London School of Hygiene and Tropical Medicine; School of Biomedical Engineering and Imaging Sciences (C.H.S.), King's College London; Centre for Medical Image Computing (C.H.S., O.G., H.P., F.B.) and Department of Population Sciences and Experimental Medicine (C.H.S.), MRC Unit for Lifelong Health and Ageing at UCL, University College London, United Kingdom; Department of Radiology and Nuclear Medicine (F.B.), VU University Medical Center, Amsterdam Neuroscience; and Department of Neurology and Neurosurgery (G.J.B.), UMC Utrecht Brain Center, University Medical Center Utrecht, the Netherlands
| | - Geert Jan Biessels
- From the Department of Neurodegenerative Disease (L.P., A.M., C.H.S., E.N.M., I.B.M., P.W., H.P., D.M.C., J.B.), Dementia Research Centre, UCL Queen Square Institute of Neurology, London; Medical Statistics (A.M.), London School of Hygiene and Tropical Medicine; School of Biomedical Engineering and Imaging Sciences (C.H.S.), King's College London; Centre for Medical Image Computing (C.H.S., O.G., H.P., F.B.) and Department of Population Sciences and Experimental Medicine (C.H.S.), MRC Unit for Lifelong Health and Ageing at UCL, University College London, United Kingdom; Department of Radiology and Nuclear Medicine (F.B.), VU University Medical Center, Amsterdam Neuroscience; and Department of Neurology and Neurosurgery (G.J.B.), UMC Utrecht Brain Center, University Medical Center Utrecht, the Netherlands
| | - David M Cash
- From the Department of Neurodegenerative Disease (L.P., A.M., C.H.S., E.N.M., I.B.M., P.W., H.P., D.M.C., J.B.), Dementia Research Centre, UCL Queen Square Institute of Neurology, London; Medical Statistics (A.M.), London School of Hygiene and Tropical Medicine; School of Biomedical Engineering and Imaging Sciences (C.H.S.), King's College London; Centre for Medical Image Computing (C.H.S., O.G., H.P., F.B.) and Department of Population Sciences and Experimental Medicine (C.H.S.), MRC Unit for Lifelong Health and Ageing at UCL, University College London, United Kingdom; Department of Radiology and Nuclear Medicine (F.B.), VU University Medical Center, Amsterdam Neuroscience; and Department of Neurology and Neurosurgery (G.J.B.), UMC Utrecht Brain Center, University Medical Center Utrecht, the Netherlands
| | - Josephine Barnes
- From the Department of Neurodegenerative Disease (L.P., A.M., C.H.S., E.N.M., I.B.M., P.W., H.P., D.M.C., J.B.), Dementia Research Centre, UCL Queen Square Institute of Neurology, London; Medical Statistics (A.M.), London School of Hygiene and Tropical Medicine; School of Biomedical Engineering and Imaging Sciences (C.H.S.), King's College London; Centre for Medical Image Computing (C.H.S., O.G., H.P., F.B.) and Department of Population Sciences and Experimental Medicine (C.H.S.), MRC Unit for Lifelong Health and Ageing at UCL, University College London, United Kingdom; Department of Radiology and Nuclear Medicine (F.B.), VU University Medical Center, Amsterdam Neuroscience; and Department of Neurology and Neurosurgery (G.J.B.), UMC Utrecht Brain Center, University Medical Center Utrecht, the Netherlands
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Camino-Pontes B, Gonzalez-Lopez F, Santamaría-Gomez G, Sutil-Jimenez AJ, Sastre-Barrios C, de Pierola IF, Cortes JM. One-year prediction of cognitive decline following cognitive-stimulation from real-world data. J Neuropsychol 2023. [PMID: 36727214 DOI: 10.1111/jnp.12307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/09/2023] [Accepted: 01/17/2023] [Indexed: 02/03/2023]
Abstract
Clinical evidence based on real-world data (RWD) is accumulating exponentially providing larger sample sizes available, which demand novel methods to deal with the enhanced heterogeneity of the data. Here, we used RWD to assess the prediction of cognitive decline in a large heterogeneous sample of participants being enrolled with cognitive stimulation, a phenomenon that is of great interest to clinicians but that is riddled with difficulties and limitations. More precisely, from a multitude of neuropsychological Training Materials (TMs), we asked whether was possible to accurately predict an individual's cognitive decline one year after being tested. In particular, we performed longitudinal modelling of the scores obtained from 215 different tests, grouped into 29 cognitive domains, a total of 124,610 instances from 7902 participants (40% male, 46% female, 14% not indicated), each performing an average of 16 tests. Employing a machine learning approach based on ROC analysis and cross-validation techniques to overcome overfitting, we show that different TMs belonging to several cognitive domains can accurately predict cognitive decline, while other domains perform poorly, suggesting that the ability to predict decline one year later is not specific to any particular domain, but is rather widely distributed across domains. Moreover, when addressing the same problem between individuals with a common diagnosed label, we found that some domains had more accurate classification for conditions such as Parkinson's disease and Down syndrome, whereas they are less accurate for Alzheimer's disease or multiple sclerosis. Future research should combine similar approaches to ours with standard neuropsychological measurements to enhance interpretability and the possibility of generalizing across different cohorts.
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Affiliation(s)
| | | | | | | | | | | | - Jesus M Cortes
- Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain.,IKERBASQUE: The Basque Foundation for Science, Bilbao, Spain.,Department of Cell Biology and Histology, University of the Basque Country, Leioa, Spain
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Classification of Initial Stages of Alzheimer’s Disease through Pet Neuroimaging Modality and Deep Learning: Quantifying the Impact of Image Filtering Approaches. MATHEMATICS 2021. [DOI: 10.3390/math9233101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alzheimer’s disease (AD) is a leading health concern affecting the elderly population worldwide. It is defined by amyloid plaques, neurofibrillary tangles, and neuronal loss. Neuroimaging modalities such as positron emission tomography (PET) and magnetic resonance imaging are routinely used in clinical settings to monitor the alterations in the brain during the course of progression of AD. Deep learning techniques such as convolutional neural networks (CNNs) have found numerous applications in healthcare and other technologies. Together with neuroimaging modalities, they can be deployed in clinical settings to learn effective representations of data for different tasks such as classification, segmentation, detection, etc. Image filtering methods are instrumental in making images viable for image processing operations and have found numerous applications in image-processing-related tasks. In this work, we deployed 3D-CNNs to learn effective representations of PET modality data to quantify the impact of different image filtering approaches. We used box filtering, median filtering, Gaussian filtering, and modified Gaussian filtering approaches to preprocess the images and use them for classification using 3D-CNN architecture. Our findings suggest that these approaches are nearly equivalent and have no distinct advantage over one another. For the multiclass classification task between normal control (NC), mild cognitive impairment (MCI), and AD classes, the 3D-CNN architecture trained using Gaussian-filtered data performed the best. For binary classification between NC and MCI classes, the 3D-CNN architecture trained using median-filtered data performed the best, while, for binary classification between AD and MCI classes, the 3D-CNN architecture trained using modified Gaussian-filtered data performed the best. Finally, for binary classification between AD and NC classes, the 3D-CNN architecture trained using box-filtered data performed the best.
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Fabrizio C, Termine A, Caltagirone C, Sancesario G. Artificial Intelligence for Alzheimer's Disease: Promise or Challenge? Diagnostics (Basel) 2021; 11:1473. [PMID: 34441407 PMCID: PMC8391160 DOI: 10.3390/diagnostics11081473] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 01/23/2023] Open
Abstract
Decades of experimental and clinical research have contributed to unraveling many mechanisms in the pathogenesis of Alzheimer's disease (AD), but the puzzle is still incomplete. Although we can suppose that there is no complete set of puzzle pieces, the recent growth of open data-sharing initiatives collecting lifestyle, clinical, and biological data from AD patients has provided a potentially unlimited amount of information about the disease, far exceeding the human ability to make sense of it. Moreover, integrating Big Data from multi-omics studies provides the potential to explore the pathophysiological mechanisms of the entire biological continuum of AD. In this context, Artificial Intelligence (AI) offers a wide variety of methods to analyze large and complex data in order to improve knowledge in the AD field. In this review, we focus on recent findings and future challenges for AI in AD research. In particular, we discuss the use of Computer-Aided Diagnosis tools for AD diagnosis and the use of AI to potentially support clinical practices for the prediction of individual risk of AD conversion as well as patient stratification in order to finally develop effective and personalized therapies.
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Affiliation(s)
- Carlo Fabrizio
- Laboratory of Experimental and Behavioral Neurophysiology, IRCCS Santa Lucia Foundation, 00143 Rome, Italy; (C.F.); (A.T.)
| | - Andrea Termine
- Laboratory of Experimental and Behavioral Neurophysiology, IRCCS Santa Lucia Foundation, 00143 Rome, Italy; (C.F.); (A.T.)
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, 00179 Rome, Italy;
| | - Giulia Sancesario
- Biobank, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
- European Center for Brain Research, Experimental Neuroscience, 00143 Rome, Italy
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López ME, Turrero A, Cuesta P, Rodríguez-Rojo IC, Barabash A, Marcos A, Maestú F, Fernández A. A multivariate model of time to conversion from mild cognitive impairment to Alzheimer's disease. GeroScience 2020; 42:1715-1732. [PMID: 32886293 PMCID: PMC7732920 DOI: 10.1007/s11357-020-00260-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/24/2020] [Indexed: 11/26/2022] Open
Abstract
The present study was aimed at determining which combination of demographic, genetic, cognitive, neurophysiological, and neuroanatomical factors may predict differences in time to progression from mild cognitive impairment (MCI) to Alzheimer's disease (AD). To this end, a sample of 121 MCIs was followed up during a 5-year period. According to their clinical outcome, MCIs were divided into two subgroups: (i) the "progressive" MCI group (n = 46; mean time to progression 17 ± 9.73 months) and (ii) the "stable" MCI group (n = 75; mean time of follow-up 31.37 ± 14.58 months). Kaplan-Meier survival analyses were applied to explore each variable's relationship with the progression to AD. Once potential predictors were detected, Cox regression analyses were utilized to calculate a parsimonious model to estimate differences in time to progression. The final model included three variables (in order of relevance): left parahippocampal volume (corrected by intracranial volume, LP_ ICV), delayed recall (DR), and left inferior occipital lobe individual alpha peak frequency (LIOL_IAPF). Those MCIs with LP_ICV volume, DR score, and LIOL_IAPF value lower than the defined cutoff had 6 times, 5.5 times, and 3 times higher risk of progression to AD, respectively. Besides, when the categories of the three variables were "unfavorable" (i.e., values below the cutoff), 100% of cases progressed to AD at the end of follow-up. Our results highlighted the relevance of neurophysiological markers as predictors of conversion (LIOL_IAPF) and the importance of multivariate models that combine markers of different nature to predict time to progression from MCI to dementia.
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Affiliation(s)
- María Eugenia López
- Department of Experimental Psychology, Cognitive Processes and Speech Therapy, Complutense University of Madrid, Madrid, Spain.
- Laboratory of Cognitive and Computational Neuroscience, Center for Biomedical Technology, Complutense University of Madrid and Polytechnic University of Madrid, Madrid, Spain.
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain.
- Institute of Sanitary Investigation (IdISSC), San Carlos University Hospital, Madrid, Spain.
| | - Agustín Turrero
- Institute of Sanitary Investigation (IdISSC), San Carlos University Hospital, Madrid, Spain
- Department of Statistics and Operational Research, Complutense University of Madrid, Madrid, Spain
| | - Pablo Cuesta
- Department of Experimental Psychology, Cognitive Processes and Speech Therapy, Complutense University of Madrid, Madrid, Spain
- Laboratory of Cognitive and Computational Neuroscience, Center for Biomedical Technology, Complutense University of Madrid and Polytechnic University of Madrid, Madrid, Spain
| | - Inmaculada Concepción Rodríguez-Rojo
- Laboratory of Cognitive and Computational Neuroscience, Center for Biomedical Technology, Complutense University of Madrid and Polytechnic University of Madrid, Madrid, Spain
- Psychology Faculty, Centro Universitario Villanueva, Madrid, Spain
- Physiotherapy and Nursing Faculty, University of Castilla-La Mancha, Toledo, Spain
| | - Ana Barabash
- Institute of Sanitary Investigation (IdISSC), San Carlos University Hospital, Madrid, Spain
- Laboratory of Psychoneuroendocrinology and Genetics, San Carlos University Hospital, Madrid, Spain
| | - Alberto Marcos
- Institute of Sanitary Investigation (IdISSC), San Carlos University Hospital, Madrid, Spain
- Neurology Department, San Carlos University Hospital, Madrid, Spain
| | - Fernando Maestú
- Department of Experimental Psychology, Cognitive Processes and Speech Therapy, Complutense University of Madrid, Madrid, Spain
- Laboratory of Cognitive and Computational Neuroscience, Center for Biomedical Technology, Complutense University of Madrid and Polytechnic University of Madrid, Madrid, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
- Institute of Sanitary Investigation (IdISSC), San Carlos University Hospital, Madrid, Spain
| | - Alberto Fernández
- Laboratory of Cognitive and Computational Neuroscience, Center for Biomedical Technology, Complutense University of Madrid and Polytechnic University of Madrid, Madrid, Spain
- Institute of Sanitary Investigation (IdISSC), San Carlos University Hospital, Madrid, Spain
- Department of Legal Medicine, Psychiatry and Pathology, Complutense University of Madrid, Madrid, Spain
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Golriz Khatami S, Robinson C, Birkenbihl C, Domingo-Fernández D, Hoyt CT, Hofmann-Apitius M. Challenges of Integrative Disease Modeling in Alzheimer's Disease. Front Mol Biosci 2020; 6:158. [PMID: 31993440 PMCID: PMC6971060 DOI: 10.3389/fmolb.2019.00158] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/18/2019] [Indexed: 12/15/2022] Open
Abstract
Dementia-related diseases like Alzheimer's Disease (AD) have a tremendous social and economic cost. A deeper understanding of its underlying pathophysiologies may provide an opportunity for earlier detection and therapeutic intervention. Previous approaches for characterizing AD were targeted at single aspects of the disease. Yet, due to the complex nature of AD, the success of these approaches was limited. However, in recent years, advancements in integrative disease modeling, built on a wide range of AD biomarkers, have taken a global view on the disease, facilitating more comprehensive analysis and interpretation. Integrative AD models can be sorted in two primary types, namely hypothetical models and data-driven models. The latter group split into two subgroups: (i) Models that use traditional statistical methods such as linear models, (ii) Models that take advantage of more advanced artificial intelligence approaches such as machine learning. While many integrative AD models have been published over the last decade, their impact on clinical practice is limited. There exist major challenges in the course of integrative AD modeling, namely data missingness and censoring, imprecise human-involved priori knowledge, model reproducibility, dataset interoperability, dataset integration, and model interpretability. In this review, we highlight recent advancements and future possibilities of integrative modeling in the field of AD research, showcase and discuss the limitations and challenges involved, and finally, propose avenues to address several of these challenges.
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Affiliation(s)
- Sepehr Golriz Khatami
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Christine Robinson
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Colin Birkenbihl
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Daniel Domingo-Fernández
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Charles Tapley Hoyt
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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Li K, Luo S. Dynamic prediction of Alzheimer's disease progression using features of multiple longitudinal outcomes and time-to-event data. Stat Med 2019; 38:4804-4818. [PMID: 31386218 DOI: 10.1002/sim.8334] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/19/2019] [Accepted: 07/02/2019] [Indexed: 12/16/2022]
Abstract
This paper is motivated by combining serial neurocognitive assessments and other clinical variables for monitoring the progression of Alzheimer's disease (AD). We propose a novel framework for the use of multiple longitudinal neurocognitive markers to predict the progression of AD. The conventional joint modeling longitudinal and survival data approach is not applicable when there is a large number of longitudinal outcomes. We introduce various approaches based on functional principal component for dimension reduction and feature extraction from multiple longitudinal outcomes. We use these features to extrapolate the health outcome trajectories and use scores on these features as predictors in a Cox proportional hazards model to conduct predictions over time. We propose a personalized dynamic prediction framework that can be updated as new observations collected to reflect the patient's latest prognosis, and thus intervention could be initiated in a timely manner. Simulation studies and application to the Alzheimer's Disease Neuroimaging Initiative dataset demonstrate the robustness of the method for the prediction of future health outcomes and risks of target events under various scenarios.
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Affiliation(s)
- Kan Li
- Merck Research Lab, Merck & Co, North Wales, Pennsylvania
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina
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A deep learning model for early prediction of Alzheimer's disease dementia based on hippocampal magnetic resonance imaging data. Alzheimers Dement 2019; 15:1059-1070. [PMID: 31201098 DOI: 10.1016/j.jalz.2019.02.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 02/14/2019] [Accepted: 02/25/2019] [Indexed: 02/04/2023]
Abstract
INTRODUCTION It is challenging at baseline to predict when and which individuals who meet criteria for mild cognitive impairment (MCI) will ultimately progress to Alzheimer's disease (AD) dementia. METHODS A deep learning method is developed and validated based on magnetic resonance imaging scans of 2146 subjects (803 for training and 1343 for validation) to predict MCI subjects' progression to AD dementia in a time-to-event analysis setting. RESULTS The deep-learning time-to-event model predicted individual subjects' progression to AD dementia with a concordance index of 0.762 on 439 Alzheimer's Disease Neuroimaging Initiative testing MCI subjects with follow-up duration from 6 to 78 months (quartiles: [24, 42, 54]) and a concordance index of 0.781 on 40 Australian Imaging Biomarkers and Lifestyle Study of Aging testing MCI subjects with follow-up duration from 18 to 54 months (quartiles: [18, 36, 54]). The predicted progression risk also clustered individual subjects into subgroups with significant differences in their progression time to AD dementia (P < .0002). Improved performance for predicting progression to AD dementia (concordance index = 0.864) was obtained when the deep learning-based progression risk was combined with baseline clinical measures. DISCUSSION Our method provides a cost effective and accurate means for prognosis and potentially to facilitate enrollment in clinical trials with individuals likely to progress within a specific temporal period.
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Li K, Luo S. Bayesian Functional Joint Models for Multivariate Longitudinal and Time-to-Event Data. Comput Stat Data Anal 2018; 129:14-29. [PMID: 30559575 DOI: 10.1016/j.csda.2018.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A multivariate functional joint model framework is proposed which enables the repeatedly measured functional outcomes, scalar outcomes, and survival process to be modeled simultaneously while accounting for association among the multiple (functional and scalar) longitudinal and survival processes. This data structure is increasingly common across medical studies of neurodegenerative diseases and is exemplified by the motivating Alzheimer's Disease Neuroimaging Initiative (ADNI) study, in which serial brain imaging, clinical and neuropsychological assessments are collected to measure the progression of Alzheimer's disease (AD). The proposed functional joint model consists of a longitudinal function-on-scalar submodel, a regular longitudinal submodel, and a survival submodel which allows time-dependent functional and scalar covariates. A Bayesian approach is adopted for parameter estimation and a dynamic prediction framework is introduced for predicting the subjects' future health outcomes and risk of AD conversion. The proposed model is evaluated by a simulation study and is applied to the motivating ADNI study.
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Affiliation(s)
- Kan Li
- Merck Research Lab, Merck & Co, 351 North Sumneytown Pike, North Wales, PA 19454, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, 2400 Pratt St, 7040 North Pavilion, Durham, NC 27705, USA
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12
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Li K, O'Brien R, Lutz M, Luo S. A prognostic model of Alzheimer's disease relying on multiple longitudinal measures and time-to-event data. Alzheimers Dement 2018; 14:644-651. [PMID: 29306668 PMCID: PMC5938096 DOI: 10.1016/j.jalz.2017.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/30/2017] [Accepted: 11/13/2017] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Characterizing progression in Alzheimer's disease is critically important for early detection and targeted treatment. The objective was to develop a prognostic model, based on multivariate longitudinal markers, for predicting progression-free survival in patients with mild cognitive impairment. METHODS The information contained in multiple longitudinal markers was extracted using multivariate functional principal components analysis and used as predictors in the Cox regression models. Cross-validation was used for selecting the best model based on Alzheimer's Disease Neuroimaging Initiative-1. External validation was conducted on Alzheimer's Disease Neuroimaging Initiative-2. RESULTS Model comparison yielded a prognostic index computed as the weighted combination of historical information of five neurocognitive longitudinal markers that are routinely collected in observational studies. The comprehensive validity analysis provided solid evidence of the usefulness of the model for predicting Alzheimer's disease progression. DISCUSSION The prognostic model was improved by incorporating multiple longitudinal markers. It is useful for monitoring disease and identifying patients for clinical trial recruitment.
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Affiliation(s)
- Kan Li
- Department of Biostatistics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Richard O'Brien
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Michael Lutz
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA.
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Kong D, Ibrahim JG, Lee E, Zhu H. FLCRM: Functional linear cox regression model. Biometrics 2017; 74:109-117. [PMID: 28863246 DOI: 10.1111/biom.12748] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 04/01/2017] [Accepted: 06/01/2017] [Indexed: 11/27/2022]
Abstract
We consider a functional linear Cox regression model for characterizing the association between time-to-event data and a set of functional and scalar predictors. The functional linear Cox regression model incorporates a functional principal component analysis for modeling the functional predictors and a high-dimensional Cox regression model to characterize the joint effects of both functional and scalar predictors on the time-to-event data. We develop an algorithm to calculate the maximum approximate partial likelihood estimates of unknown finite and infinite dimensional parameters. We also systematically investigate the rate of convergence of the maximum approximate partial likelihood estimates and a score test statistic for testing the nullity of the slope function associated with the functional predictors. We demonstrate our estimation and testing procedures by using simulations and the analysis of the Alzheimer's Disease Neuroimaging Initiative (ADNI) data. Our real data analyses show that high-dimensional hippocampus surface data may be an important marker for predicting time to conversion to Alzheimer's disease. Data used in the preparation of this article were obtained from the ADNI database (adni.loni.usc.edu).
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Affiliation(s)
- Dehan Kong
- Department of Statistical Sciences, University of Toronto, Ontario, Canada
| | - Joseph G Ibrahim
- Department of Biostatistics, University of North Carolina at Chapel Hill, North Carolina, U.S.A
| | - Eunjee Lee
- Department of Biostatistics, University of Michigan, Michigan, U.S.A
| | - Hongtu Zhu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Texas, U.S.A
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Li K, Luo S. Dynamic predictions in Bayesian functional joint models for longitudinal and time-to-event data: An application to Alzheimer's disease. Stat Methods Med Res 2017; 28:327-342. [PMID: 28750578 DOI: 10.1177/0962280217722177] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In the study of Alzheimer's disease, researchers often collect repeated measurements of clinical variables, event history, and functional data. If the health measurements deteriorate rapidly, patients may reach a level of cognitive impairment and are diagnosed as having dementia. An accurate prediction of the time to dementia based on the information collected is helpful for physicians to monitor patients' disease progression and to make early informed medical decisions. In this article, we first propose a functional joint model to account for functional predictors in both longitudinal and survival submodels in the joint modeling framework. We then develop a Bayesian approach for parameter estimation and a dynamic prediction framework for predicting the subjects' future outcome trajectories and risk of dementia, based on their scalar and functional measurements. The proposed Bayesian functional joint model provides a flexible framework to incorporate many features both in joint modeling of longitudinal and survival data and in functional data analysis. Our proposed model is evaluated by a simulation study and is applied to the motivating Alzheimer's Disease Neuroimaging Initiative study.
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Affiliation(s)
- Kan Li
- Department of Biostatistics, The University of Texas Health Science Center at Houston, Houston, USA
| | - Sheng Luo
- Department of Biostatistics, The University of Texas Health Science Center at Houston, Houston, USA
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15
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Li K, Luo S. Functional joint model for longitudinal and time-to-event data: an application to Alzheimer's disease. Stat Med 2017; 36:3560-3572. [PMID: 28664662 DOI: 10.1002/sim.7381] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 04/14/2017] [Accepted: 05/30/2017] [Indexed: 11/09/2022]
Abstract
Functional data are increasingly collected in public health and medical studies to better understand many complex diseases. Besides the functional data, other clinical measures are often collected repeatedly. Investigating the association between these longitudinal data and time to a survival event is of great interest to these studies. In this article, we develop a functional joint model (FJM) to account for functional predictors in both longitudinal and survival submodels in the joint modeling framework. The parameters of FJM are estimated in a maximum likelihood framework via expectation maximization algorithm. The proposed FJM provides a flexible framework to incorporate many features both in joint modeling of longitudinal and survival data and in functional data analysis. The FJM is evaluated by a simulation study and is applied to the Alzheimer's Disease Neuroimaging Initiative study, a motivating clinical study testing whether serial brain imaging, clinical, and neuropsychological assessments can be combined to measure the progression of Alzheimer's disease. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Kan Li
- Department of Biostatistics, The University of Texas Health Science Center at Houston, Houston, 77030, TX, U.S.A
| | - Sheng Luo
- Department of Biostatistics, The University of Texas Health Science Center at Houston, Houston, 77030, TX, U.S.A
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Liu K, Chen K, Yao L, Guo X. Prediction of Mild Cognitive Impairment Conversion Using a Combination of Independent Component Analysis and the Cox Model. Front Hum Neurosci 2017; 11:33. [PMID: 28220065 PMCID: PMC5292818 DOI: 10.3389/fnhum.2017.00033] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/16/2017] [Indexed: 12/13/2022] Open
Abstract
Mild cognitive impairment (MCI) represents a transitional stage from normal aging to Alzheimer’s disease (AD) and corresponds to a higher risk of developing AD. Thus, it is necessary to explore and predict the onset of AD in MCI stage. In this study, we propose a combination of independent component analysis (ICA) and the multivariate Cox proportional hazards regression model to investigate promising risk factors associated with MCI conversion among 126 MCI converters and 108 MCI non-converters from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database. Using structural magnetic resonance imaging (MRI) and fluorodeoxyglucose positron emission tomography (FDG-PET) data, we extracted brain networks from AD and normal control groups via ICA and then constructed Cox models that included network-based neuroimaging factors for the MCI group. We carried out five separate Cox analyses and the two-modality neuroimaging Cox model identified three significant network-based risk factors with higher prediction performance (accuracy = 73.50%) than those in either single-modality model (accuracy = 68.80%). Additionally, the results of the comprehensive Cox model, including significant neuroimaging factors and clinical variables, demonstrated that MCI individuals with reduced gray matter volume in a temporal lobe-related network of structural MRI [hazard ratio (HR) = 8.29E-05 (95% confidence interval (CI), 5.10E- 07 ~ 0.013)], low glucose metabolism in the posterior default mode network based on FDG-PET [HR = 0.066 (95% CI, 4.63E-03 ~ 0.928)], positive apolipoprotein E ε4-status [HR = 1. 988 (95% CI, 1.531 ~ 2.581)], increased Alzheimer’s Disease Assessment Scale-Cognitive Subscale scores [HR = 1.100 (95% CI, 1.059 ~ 1.144)] and Sum of Boxes of Clinical Dementia Rating scores [HR = 1.622 (95% CI, 1.364 ~ 1.930)] were more likely to convert to AD within 36 months after baselines. These significant risk factors in such comprehensive Cox model had the best prediction ability (accuracy = 84.62%, sensitivity = 86.51%, specificity = 82.41%) compared to either neuroimaging factors or clinical variables alone. These results suggested that a combination of ICA and Cox model analyses could be used successfully in survival analysis and provide a network-based perspective of MCI progression or AD-related studies.
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Affiliation(s)
- Ke Liu
- College of Information Science and Technology, Beijing Normal University Beijing, China
| | - Kewei Chen
- Banner Alzheimer's Institute and Banner Good Samaritan PET Center, Phoenix AZ, USA
| | - Li Yao
- College of Information Science and Technology, Beijing Normal University Beijing, China
| | - Xiaojuan Guo
- College of Information Science and Technology, Beijing Normal University Beijing, China
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Li K, Chan W, Doody RS, Quinn J, Luo S. Prediction of Conversion to Alzheimer's Disease with Longitudinal Measures and Time-To-Event Data. J Alzheimers Dis 2017; 58:361-371. [PMID: 28436391 PMCID: PMC5477671 DOI: 10.3233/jad-161201] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND Identifying predictors of conversion to Alzheimer's disease (AD) is critically important for AD prevention and targeted treatment. OBJECTIVE To compare various clinical and biomarker trajectories for tracking progression and predicting conversion from amnestic mild cognitive impairment to probable AD. METHODS Participants were from the ADNI-1 study. We assessed the ability of 33 longitudinal biomarkers to predict time to AD conversion, accounting for demographic and genetic factors. We used joint modelling of longitudinal and survival data to examine the association between changes of measures and disease progression. We also employed time-dependent receiver operating characteristic method to assess the discriminating capability of the measures. RESULTS 23 of 33 longitudinal clinical and imaging measures are significant predictors of AD conversion beyond demographic and genetic factors. The strong phenotypic and biological predictors are in the cognitive domain (ADAS-Cog; RAVLT), functional domain (FAQ), and neuroimaging domain (middle temporal gyrus and hippocampal volume). The strongest predictor is ADAS-Cog 13 with an increase of one SD in ADAS-Cog 13 increased the risk of AD conversion by 2.92 times. CONCLUSION Prediction of AD conversion can be improved by incorporating longitudinal change information, in addition to baseline characteristics. Cognitive measures are consistently significant and generally stronger predictors than imaging measures.
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Affiliation(s)
- Kan Li
- Department of Biostatistics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Wenyaw Chan
- Department of Biostatistics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Joseph Quinn
- Department of Neurology, Oregon Health and Science University and Portland VA Medical Center, Portland, OR, USA
| | - Sheng Luo
- Department of Biostatistics, The University of Texas Health Science Center at Houston, Houston, TX, USA
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Li X, Gao Y, Meng Z, Zhang C, Qi Q. Regulatory role of microRNA-30b and plasminogen activator inhibitor-1 in the pathogenesis of cognitive impairment. Exp Ther Med 2016; 11:1993-1998. [PMID: 27168840 DOI: 10.3892/etm.2016.3162] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 01/15/2016] [Indexed: 02/06/2023] Open
Abstract
The present study aimed to investigate the role of plasminogen activator inhibitor-1 (PAI-1) in drug-induced early cognitive impairment and the underlying mechanism concerning microRNA (miR)-30b. A mouse model of cognitive impairment was established by intraperitoneal injection of scopolamine (2 mg/kg body weight) for 13 days. Behavioral performance was assessed using the Morris water maze (MWM) test. The mRNA expression levels of PAI-1 and miR-30b were detected using quantitative polymerase chain reaction (qPCR). The protein expression levels of PAI-1 in the hippocampus and blood were determined using western blot analysis and enzyme-linked immunosorbent assays. The MWM test demonstrated that, on days 3 and 4, the escape latency was significantly elevated in the model mice in comparison with control group (P<0.05). In addition, the length of swimming path was significantly increased (P<0.05), while the number of times of crossing the platform location was significantly reduced in the model mouse group (P<0.05) in comparison with the control group. qPCR demonstrated that the mRNA expression levels of PAI-1 in the model mice was significantly elevated in the hippocampus and blood in comparison with the control group (P<0.01). Furthermore, western blot analysis and enzyme-linked immunosorbent assay demonstrated that the protein expression levels of PAI-1 were significantly elevated in the hippocampus and blood in the model group, in comparison with the control group (P<0.05). Notably, the levels of miR-30b in the hippocampus and blood were significantly decreased in the model mice in comparison with the control group (P<0.01). To conclude, the expression levels of PAI-1 were significantly elevated in mice with scopolamine-induced cognitive impairment, which may be associated with the downregulation of miR-30b. The findings from the present study suggest that miR-30b may be involved in the regulation of PAI-1, which would contribute to the pathogenesis of cognitive impairment.
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Affiliation(s)
- Xiuqin Li
- Second Department of Health, Laiwu Hospital Affiliated to Taishan Medical University, Laiwu, Shandong 271100, P.R. China
| | - Yong Gao
- Department of Neurosurgery, Laiwu Hospital Affiliated to Taishan Medical University, Laiwu, Shandong 271100, P.R. China
| | - Zhaoyun Meng
- Second Department of Health, Laiwu Hospital Affiliated to Taishan Medical University, Laiwu, Shandong 271100, P.R. China
| | - Cui Zhang
- Department of Neurology, Laiwu Hospital Affiliated to Taishan Medical University, Laiwu, Shandong 271100, P.R. China
| | - Qinde Qi
- Department of Neurology, Laiwu Hospital Affiliated to Taishan Medical University, Laiwu, Shandong 271100, P.R. China
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Lee E, Zhu H, Kong D, Wang Y, Giovanello KS, Ibrahim JG. BFLCRM: A BAYESIAN FUNCTIONAL LINEAR COX REGRESSION MODEL FOR PREDICTING TIME TO CONVERSION TO ALZHEIMER'S DISEASE. Ann Appl Stat 2015; 9:2153-2178. [PMID: 26900412 DOI: 10.1214/15-aoas879] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The aim of this paper is to develop a Bayesian functional linear Cox regression model (BFLCRM) with both functional and scalar covariates. This new development is motivated by establishing the likelihood of conversion to Alzheimer's disease (AD) in 346 patients with mild cognitive impairment (MCI) enrolled in the Alzheimer's Disease Neuroimaging Initiative 1 (ADNI-1) and the early markers of conversion. These 346 MCI patients were followed over 48 months, with 161 MCI participants progressing to AD at 48 months. The functional linear Cox regression model was used to establish that functional covariates including hippocampus surface morphology and scalar covariates including brain MRI volumes, cognitive performance (ADAS-Cog), and APOE status can accurately predict time to onset of AD. Posterior computation proceeds via an efficient Markov chain Monte Carlo algorithm. A simulation study is performed to evaluate the finite sample performance of BFLCRM.
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Affiliation(s)
- Eunjee Lee
- Departments of Statistics and Operation Research, Biostatistics, and Psychology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hongtu Zhu
- Departments of Statistics and Operation Research, Biostatistics, and Psychology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dehan Kong
- Departments of Statistics and Operation Research, Biostatistics, and Psychology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering Arizona State University Tempe, AZ 85287-8809
| | - Kelly Sullivan Giovanello
- Departments of Statistics and Operation Research, Biostatistics, and Psychology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joseph G Ibrahim
- Departments of Statistics and Operation Research, Biostatistics, and Psychology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Bonner-Jackson A, Mahmoud S, Miller J, Banks SJ. Verbal and non-verbal memory and hippocampal volumes in a memory clinic population. ALZHEIMERS RESEARCH & THERAPY 2015; 7:61. [PMID: 26468086 PMCID: PMC4607093 DOI: 10.1186/s13195-015-0147-9] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 09/14/2015] [Indexed: 01/04/2023]
Abstract
Introduction Better characterization of the relationship between episodic memory and hippocampal volumes is crucial in early detection of neurodegenerative disease. We examined these relationships in a memory clinic population. Methods Participants (n = 226) underwent structural magnetic resonance imaging and tests of verbal (Hopkins Verbal Learning Test-Revised, HVLT-R) and non-verbal (Brief Visuospatial Memory Test-Revised, BVMT-R) memory. Correlational analyses were performed, and analyses on clinical subgroups (i.e., amnestic Mild Cognitive Impairment, non-amnestic Mild Cognitive Impairment, probable Alzheimer’s disease, intact memory) were conducted. Results Positive associations were identified between bilateral hippocampal volumes and both memory measures, and BVMT-R learning slope was more strongly positively associated with hippocampal volumes than HVLT-R learning slope. Amnestic Mild Cognitive Impairment (aMCI) participants showed specific positive associations between BVMT-R performance and hippocampal volumes bilaterally. Additionally, analyses of the aMCI group showed trend-level evidence of material-specific lateralization, such that retention of verbal information was positively associated with left hippocampal volume, whereas learning curve and retention of non-verbal information was positively associated with right hippocampal volume. Conclusions Findings support the link between episodic memory and hippocampal volumes in a memory clinic population. Non-verbal memory measures also may have higher diagnostic value, particularly in individuals at elevated risk for Alzheimer’s disease.
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Affiliation(s)
- Aaron Bonner-Jackson
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, 9500 Euclid Avenue/U10, Cleveland, OH, 44195, USA.
| | - Shamseldeen Mahmoud
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, 9500 Euclid Avenue/U10, Cleveland, OH, 44195, USA.
| | - Justin Miller
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Las Vegas, NV, USA.
| | - Sarah J Banks
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Las Vegas, NV, USA.
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Nalls MA, McLean CY, Rick J, Eberly S, Hutten SJ, Gwinn K, Sutherland M, Martinez M, Heutink P, Williams NM, Hardy J, Gasser T, Brice A, Price TR, Nicolas A, Keller MF, Molony C, Gibbs JR, Chen-Plotkin A, Suh E, Letson C, Fiandaca MS, Mapstone M, Federoff HJ, Noyce AJ, Morris H, Van Deerlin VM, Weintraub D, Zabetian C, Hernandez DG, Lesage S, Mullins M, Conley ED, Northover CAM, Frasier M, Marek K, Day-Williams AG, Stone DJ, Ioannidis JPA, Singleton AB. Diagnosis of Parkinson's disease on the basis of clinical and genetic classification: a population-based modelling study. Lancet Neurol 2015; 14:1002-9. [PMID: 26271532 PMCID: PMC4575273 DOI: 10.1016/s1474-4422(15)00178-7] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/23/2015] [Accepted: 07/07/2015] [Indexed: 02/03/2023]
Abstract
BACKGROUND Accurate diagnosis and early detection of complex diseases, such as Parkinson's disease, has the potential to be of great benefit for researchers and clinical practice. We aimed to create a non-invasive, accurate classification model for the diagnosis of Parkinson's disease, which could serve as a basis for future disease prediction studies in longitudinal cohorts. METHODS We developed a model for disease classification using data from the Parkinson's Progression Marker Initiative (PPMI) study for 367 patients with Parkinson's disease and phenotypically typical imaging data and 165 controls without neurological disease. Olfactory function, genetic risk, family history of Parkinson's disease, age, and gender were algorithmically selected by stepwise logistic regression as significant contributors to our classifying model. We then tested the model with data from 825 patients with Parkinson's disease and 261 controls from five independent cohorts with varying recruitment strategies and designs: the Parkinson's Disease Biomarkers Program (PDBP), the Parkinson's Associated Risk Study (PARS), 23andMe, the Longitudinal and Biomarker Study in PD (LABS-PD), and the Morris K Udall Parkinson's Disease Research Center of Excellence cohort (Penn-Udall). Additionally, we used our model to investigate patients who had imaging scans without evidence of dopaminergic deficit (SWEDD). FINDINGS In the population from PPMI, our initial model correctly distinguished patients with Parkinson's disease from controls at an area under the curve (AUC) of 0·923 (95% CI 0·900-0·946) with high sensitivity (0·834, 95% CI 0·711-0·883) and specificity (0·903, 95% CI 0·824-0·946) at its optimum AUC threshold (0·655). All Hosmer-Lemeshow simulations suggested that when parsed into random subgroups, the subgroup data matched that of the overall cohort. External validation showed good classification of Parkinson's disease, with AUCs of 0·894 (95% CI 0·867-0·921) in the PDBP cohort, 0·998 (0·992-1·000) in PARS, 0·955 (no 95% CI available) in 23andMe, 0·929 (0·896-0·962) in LABS-PD, and 0·939 (0·891-0·986) in the Penn-Udall cohort. Four of 17 SWEDD participants who our model classified as having Parkinson's disease converted to Parkinson's disease within 1 year, whereas only one of 38 SWEDD participants who were not classified as having Parkinson's disease underwent conversion (test of proportions, p=0·003). INTERPRETATION Our model provides a potential new approach to distinguish participants with Parkinson's disease from controls. If the model can also identify individuals with prodromal or preclinical Parkinson's disease in prospective cohorts, it could facilitate identification of biomarkers and interventions. FUNDING National Institute on Aging, National Institute of Neurological Disorders and Stroke, and the Michael J Fox Foundation.
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Affiliation(s)
- Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Jacqueline Rick
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Shirley Eberly
- Deptartment of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Samantha J Hutten
- The Michael J Fox Foundation for Parkinson's Research, New York, NY 10018, USA
| | - Katrina Gwinn
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Margaret Sutherland
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Maria Martinez
- INSERM, UMR 1043, Centre de Physiopathologie de Toulouse-Purpan, Toulouse, France; Paul Sabatier University, Toulouse, France
| | - Peter Heutink
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Nigel M Williams
- Institute of Psychological Medicine and Clinical Neurosciences, MRCCentre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - John Hardy
- Reta Lila Weston Institute, University College London Institute of Neurology, London, UK
| | - Thomas Gasser
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Alexis Brice
- Sorbonne Université, UPMC Univ Paris 06, UM 1127, ICM, Paris, France; INSERM, U 1127, and CNRS, UMR 7225, Institut du Cerveau et de la Moelle Epinière, Paris, France; AP-HP, Hôpital de la Salpêtrière, Département de Génétique et Cytogénétique, Paris, France
| | - T Ryan Price
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Aude Nicolas
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Margaux F Keller
- Genetics and Pharmacogenomics, Merck Research Laboratories, West Point, PA, USA; Merck Research Laboratories, Boston, MA, USA
| | - Cliona Molony
- Genetics and Pharmacogenomics, Merck Research Laboratories, West Point, PA, USA; Merck Research Laboratories, Boston, MA, USA
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Alice Chen-Plotkin
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Eunran Suh
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher Letson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Massimo S Fiandaca
- Department of Neurology, Georgetown University Medical Center, Washington, DC, USA
| | - Mark Mapstone
- Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Howard J Federoff
- Department of Neurology, Georgetown University Medical Center, Washington, DC, USA
| | - Alastair J Noyce
- Reta Lila Weston Institute, University College London Institute of Neurology, London, UK
| | - Huw Morris
- Reta Lila Weston Institute, University College London Institute of Neurology, London, UK
| | - Vivianna M Van Deerlin
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Weintraub
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Cyrus Zabetian
- Department of Neurology, Division of Neurogenetics, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Suzanne Lesage
- Sorbonne Université, UPMC Univ Paris 06, UM 1127, ICM, Paris, France; INSERM, U 1127, and CNRS, UMR 7225, Institut du Cerveau et de la Moelle Epinière, Paris, France; AP-HP, Hôpital de la Salpêtrière, Département de Génétique et Cytogénétique, Paris, France
| | | | | | | | - Mark Frasier
- The Michael J Fox Foundation for Parkinson's Research, New York, NY 10018, USA
| | - Ken Marek
- Institute for Neurodegenerative Disorders, New Haven, CT, USA
| | | | - David J Stone
- Genetics and Pharmacogenomics, Merck Research Laboratories, West Point, PA, USA; Merck Research Laboratories, Boston, MA, USA
| | - John P A Ioannidis
- Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, CA, USA; Department of Medicine, Stanford Prevention Research Center, Stanford, CA, USA; Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, USA; Department of Statistics, Stanford University School of Humanities and Sciences, Stanford, CA, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
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Quantification of microRNA-210 in the cerebrospinal fluid and serum: Implications for Alzheimer's disease. Exp Ther Med 2015; 9:1013-1017. [PMID: 25667669 PMCID: PMC4316946 DOI: 10.3892/etm.2015.2179] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 11/18/2014] [Indexed: 12/15/2022] Open
Abstract
The aim of the present study was to investigate the potential clinical application of the genetic marker microRNA (miRNA)-210 in the cerebrospinal fluid (CSF) and serum of patients with Alzheimer’s disease (AD). The enrolled patients were divided into the mild cognitive impairment (MCI) and AD groups. Healthy individuals were used as the controls. The mRNA and protein expression of vascular endothelial growth factor (VEGF) in the CSF and serum samples was detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot analysis, respectively. The expression of miRNA-210 in the CSF and serum was detected by RT-qPCR. The results revealed that the mRNA and protein expression levels of VEGF in the CSF and serum were decreased in the MCI and AD groups compared with those in the control group. The greater the severity of the dementia, the lower the mRNA and protein expression of VEGF. Similar to the trend observed for VEGF, the miRNA-210 expression in the CSF and serum decreased as the severity of the AD increased. miRNA-210 is thus not only indicative of AD pathogenesis, but may also provide novel insights into the prevention and treatment of the disease.
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