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Kim H, Tian Y, Jung SM, Park S, Rhee HY, Ryu C, Jahng G. Predicting the apolipoprotein E ε4 allele carrier status based on gray matter volumes and cognitive function. Brain Behav 2024; 14:e3381. [PMID: 38376028 PMCID: PMC10772845 DOI: 10.1002/brb3.3381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Apolipoprotein E (ApoE) ε4 carriers have a higher risk of developing Alzheimer's disease (AD) and show brain atrophy and cognitive decline even before diagnosis. OBJECTIVE To predict ApoE ε4 status using gray matter volume (GMV) obtained from magnetic resonance imaging images and demographic data with machine learning (ML) methods. METHODS We recruited 74 participants (25 probable AD, 24 amnestic mild cognitive impairment, and 25 cognitively normal older people) with known ApoE genotype (22 ApoE ε4 carriers and 52 noncarriers) and scanned them with three-dimensional (3D) T1-weighted (T1W) and 3D double inversion recovery (DIR) sequences. We extracted GMV from regions of interest related to AD pathology and used them as features along with age and mini-mental state examination (MMSE) scores to train different ML models. We performed both receiver operating characteristic curve analysis and the prediction analysis of the ApoE ε4 carrier with different ML models. RESULTS The best model of ML analyses was a cubic support vector machine (SVM3) that used age, the MMSE score, and DIR GMVs at the amygdala, hippocampus, and precuneus as features (AUC = .88). This model outperformed models using T1W GMV or demographic data alone. CONCLUSION Our results suggest that brain atrophy with DIR GMV and cognitive decline with aging can be useful biomarkers for predicting ApoE ε4 status and identifying individuals at risk of AD progression.
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Affiliation(s)
- Hyug‐Gi Kim
- Department of RadiologyKyung Hee University HospitalSeoulRepublic of Korea
| | - Yunan Tian
- Department of Medicine, Graduate SchoolKyung Hee University College of MedicineSeoulRepublic of Korea
| | - Sue Min Jung
- Department of Biomedical Engineering, Undergraduate School, College of Electronics and InformationKyung Hee UniversityYongin‐siGyeonggi‐doRepublic of Korea
| | - Soonchan Park
- Department of RadiologyKyung Hee University Hospital at Gangdong, Kyung Hee University College of MedicineSeoulRepublic of Korea
| | - Hak Young Rhee
- Department of NeurologyKyung Hee University Hospital at Gangdong, Kyung Hee University College of MedicineSeoulRepublic of Korea
| | - Chang‐Woo Ryu
- Department of RadiologyKyung Hee University Hospital at Gangdong, Kyung Hee University College of MedicineSeoulRepublic of Korea
| | - Geon‐Ho Jahng
- Department of RadiologyKyung Hee University Hospital at Gangdong, Kyung Hee University College of MedicineSeoulRepublic of Korea
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Rui W, Zhang S, Shi H, Sheng Y, Zhu F, Yao Y, Chen X, Cheng H, Zhang Y, Aili A, Yao Z, Zhang XY, Ren Y. Deep Learning-Assisted Quantitative Susceptibility Mapping as a Tool for Grading and Molecular Subtyping of Gliomas. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:243-254. [PMID: 37325712 PMCID: PMC10260708 DOI: 10.1007/s43657-022-00087-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 11/16/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
This study aimed to explore the value of deep learning (DL)-assisted quantitative susceptibility mapping (QSM) in glioma grading and molecular subtyping. Forty-two patients with gliomas, who underwent preoperative T2 fluid-attenuated inversion recovery (T2 FLAIR), contrast-enhanced T1-weighted imaging (T1WI + C), and QSM scanning at 3.0T magnetic resonance imaging (MRI) were included in this study. Histopathology and immunohistochemistry staining were used to determine glioma grades, and isocitrate dehydrogenase (IDH) 1 and alpha thalassemia/mental retardation syndrome X-linked gene (ATRX) subtypes. Tumor segmentation was performed manually using Insight Toolkit-SNAP program (www.itksnap.org). An inception convolutional neural network (CNN) with a subsequent linear layer was employed as the training encoder to capture multi-scale features from MRI slices. Fivefold cross-validation was utilized as the training strategy (seven samples for each fold), and the ratio of sample size of the training, validation, and test dataset was 4:1:1. The performance was evaluated by the accuracy and area under the curve (AUC). With the inception CNN, single modal of QSM showed better performance in differentiating glioblastomas (GBM) and other grade gliomas (OGG, grade II-III), and predicting IDH1 mutation and ATRX loss (accuracy: 0.80, 0.77, 0.60) than either T2 FLAIR (0.69, 0.57, 0.54) or T1WI + C (0.74, 0.57, 0.46). When combining three modalities, compared with any single modality, the best AUC/accuracy/F1-scores were reached in grading gliomas (OGG and GBM: 0.91/0.89/0.87, low-grade and high-grade gliomas: 0.83/0.86/0.81), predicting IDH1 mutation (0.88/0.89/0.85), and predicting ATRX loss (0.78/0.71/0.67). As a supplement to conventional MRI, DL-assisted QSM is a promising molecular imaging method to evaluate glioma grades, IDH1 mutation, and ATRX loss. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-022-00087-6.
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Affiliation(s)
- Wenting Rui
- Department of Radiology, Huashan Hospital, Fudan University, Mid 12 Wulumuqi Road, Shanghai, 200040 China
| | - Shengjie Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433 China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433 China
| | - Huidong Shi
- Department of Radiology, Huashan Hospital, Fudan University, Mid 12 Wulumuqi Road, Shanghai, 200040 China
| | - Yaru Sheng
- Department of Radiology, Huashan Hospital, Fudan University, Mid 12 Wulumuqi Road, Shanghai, 200040 China
| | - Fengping Zhu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040 China
| | - YiDi Yao
- Department of Radiology, Huashan Hospital, Fudan University, Mid 12 Wulumuqi Road, Shanghai, 200040 China
| | - Xiang Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433 China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433 China
| | - Haixia Cheng
- Department of Neuropathology, Huashan Hospital, Fudan University, Shanghai, 200040 China
| | - Yong Zhang
- GE Healthcare, MR Research, Huatuo Road, Shanghai, 201203 China
| | - Ababikere Aili
- Department of Radiology, Kuqa County People’s Hospital, Xinjiang, 842000 China
| | - Zhenwei Yao
- Department of Radiology, Huashan Hospital, Fudan University, Mid 12 Wulumuqi Road, Shanghai, 200040 China
| | - Xiao-Yong Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433 China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433 China
| | - Yan Ren
- Department of Radiology, Huashan Hospital, Fudan University, Mid 12 Wulumuqi Road, Shanghai, 200040 China
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Uchida Y, Kan H, Sakurai K, Oishi K, Matsukawa N. Quantitative susceptibility mapping as an imaging biomarker for Alzheimer’s disease: The expectations and limitations. Front Neurosci 2022; 16:938092. [PMID: 35992906 PMCID: PMC9389285 DOI: 10.3389/fnins.2022.938092] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/14/2022] [Indexed: 11/25/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common type of dementia and a distressing diagnosis for individuals and caregivers. Researchers and clinical trials have mainly focused on β-amyloid plaques, which are hypothesized to be one of the most important factors for neurodegeneration in AD. Meanwhile, recent clinicopathological and radiological studies have shown closer associations of tau pathology rather than β-amyloid pathology with the onset and progression of Alzheimer’s symptoms. Toward a biological definition of biomarker-based research framework for AD, the 2018 National Institute on Aging–Alzheimer’s Association working group has updated the ATN classification system for stratifying disease status in accordance with relevant pathological biomarker profiles, such as cerebral β-amyloid deposition, hyperphosphorylated tau, and neurodegeneration. In addition, altered iron metabolism has been considered to interact with abnormal proteins related to AD pathology thorough generating oxidative stress, as some prior histochemical and histopathological studies supported this iron-mediated pathomechanism. Quantitative susceptibility mapping (QSM) has recently become more popular as a non-invasive magnetic resonance technique to quantify local tissue susceptibility with high spatial resolution, which is sensitive to the presence of iron. The association of cerebral susceptibility values with other pathological biomarkers for AD has been investigated using various QSM techniques; however, direct evidence of these associations remains elusive. In this review, we first briefly describe the principles of QSM. Second, we focus on a large variety of QSM applications, ranging from common applications, such as cerebral iron deposition, to more recent applications, such as the assessment of impaired myelination, quantification of venous oxygen saturation, and measurement of blood– brain barrier function in clinical settings for AD. Third, we mention the relationships among QSM, established biomarkers, and cognitive performance in AD. Finally, we discuss the role of QSM as an imaging biomarker as well as the expectations and limitations of clinically useful diagnostic and therapeutic implications for AD.
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Affiliation(s)
- Yuto Uchida
- Department of Neurology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Yuto Uchida,
| | - Hirohito Kan
- Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keita Sakurai
- Department of Radiology, National Center for Geriatrics and Gerontology, Ōbu, Japan
| | - Kenichi Oishi
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Noriyuki Matsukawa
- Department of Neurology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
- Noriyuki Matsukawa,
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Cai C, Cao J, Yang C, Chen E. Diagnosis of Amnesic Mild Cognitive Impairment Using MGS-WBC and VGBN-LM Algorithms. Front Aging Neurosci 2022; 14:893250. [PMID: 35707699 PMCID: PMC9189381 DOI: 10.3389/fnagi.2022.893250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Computer-aided diagnosis (CAD) has undergone rapid development with the advent of advanced neuroimaging and machine learning methods. Nevertheless, how to extract discriminative features from the limited and high-dimensional data is not ideal, especially for amnesic mild cognitive impairment (aMCI) data based on resting-state functional magnetic resonance imaging (rs-fMRI). Furthermore, a robust and reliable system for aMCI detection is conducive to timely detecting and screening subjects at a high risk of Alzheimer's disease (AD). In this scenario, we first develop the mask generation strategy based on within-class and between-class criterion (MGS-WBC), which primarily aims at reducing data redundancy and excavating multiscale features of the brain. Concurrently, vector generation for brain networks based on Laplacian matrix (VGBN-LM) is presented to obtain the global features of the functional network. Finally, all multiscale features are fused to further improve the diagnostic performance of aMCI. Typical classifiers for small data learning, such as naive Bayesian (NB), linear discriminant analysis (LDA), logistic regression (LR), and support vector machines (SVMs), are adopted to evaluate the diagnostic performance of aMCI. This study helps to reveal discriminative neuroimaging features, and outperforms the state-of-the-art methods, providing new insights for the intelligent construction of CAD system of aMCI.
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Affiliation(s)
- Chunting Cai
- School of Informatics, Xiamen University, Xiamen, China
| | | | - Chenhui Yang
- School of Informatics, Xiamen University, Xiamen, China
| | - E. Chen
- Department of Neurology, Zhongshan Hospital Affiliated to Xiamen University, Xiamen, China
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