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Zhou X, Chen Y, Ip FCF, Jiang Y, Cao H, Lv G, Zhong H, Chen J, Ye T, Chen Y, Zhang Y, Ma S, Lo RMN, Tong EPS, Mok VCT, Kwok TCY, Guo Q, Mok KY, Shoai M, Hardy J, Chen L, Fu AKY, Ip NY. Deep learning-based polygenic risk analysis for Alzheimer's disease prediction. Commun Med (Lond) 2023; 3:49. [PMID: 37024668 PMCID: PMC10079691 DOI: 10.1038/s43856-023-00269-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/06/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND The polygenic nature of Alzheimer's disease (AD) suggests that multiple variants jointly contribute to disease susceptibility. As an individual's genetic variants are constant throughout life, evaluating the combined effects of multiple disease-associated genetic risks enables reliable AD risk prediction. Because of the complexity of genomic data, current statistical analyses cannot comprehensively capture the polygenic risk of AD, resulting in unsatisfactory disease risk prediction. However, deep learning methods, which capture nonlinearity within high-dimensional genomic data, may enable more accurate disease risk prediction and improve our understanding of AD etiology. Accordingly, we developed deep learning neural network models for modeling AD polygenic risk. METHODS We constructed neural network models to model AD polygenic risk and compared them with the widely used weighted polygenic risk score and lasso models. We conducted robust linear regression analysis to investigate the relationship between the AD polygenic risk derived from deep learning methods and AD endophenotypes (i.e., plasma biomarkers and individual cognitive performance). We stratified individuals by applying unsupervised clustering to the outputs from the hidden layers of the neural network model. RESULTS The deep learning models outperform other statistical models for modeling AD risk. Moreover, the polygenic risk derived from the deep learning models enables the identification of disease-associated biological pathways and the stratification of individuals according to distinct pathological mechanisms. CONCLUSION Our results suggest that deep learning methods are effective for modeling the genetic risks of AD and other diseases, classifying disease risks, and uncovering disease mechanisms.
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Affiliation(s)
- Xiaopu Zhou
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
| | - Yu Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
- Chinese Academy of Sciences Key Laboratory of Brain Connectome and Manipulation, Shenzhen Key Laboratory of Translational Research for Brain Diseases, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong, 518055, China
| | - Fanny C F Ip
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
| | - Yuanbing Jiang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Han Cao
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ge Lv
- Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Huan Zhong
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Jiahang Chen
- Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tao Ye
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
- Chinese Academy of Sciences Key Laboratory of Brain Connectome and Manipulation, Shenzhen Key Laboratory of Translational Research for Brain Diseases, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong, 518055, China
| | - Yuewen Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
- Chinese Academy of Sciences Key Laboratory of Brain Connectome and Manipulation, Shenzhen Key Laboratory of Translational Research for Brain Diseases, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong, 518055, China
| | - Yulin Zhang
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
| | - Shuangshuang Ma
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
| | - Ronnie M N Lo
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Estella P S Tong
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Vincent C T Mok
- Gerald Choa Neuroscience Centre, Lui Che Woo Institute of Innovative Medicine, Therese Pei Fong Chow Research Centre for Prevention of Dementia, Division of Neurology, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Timothy C Y Kwok
- Therese Pei Fong Chow Research Centre for Prevention of Dementia, Division of Geriatrics, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Qihao Guo
- Department of Gerontology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Kin Y Mok
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - Maryam Shoai
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - John Hardy
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
- HKUST Jockey Club Institute for Advanced Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Lei Chen
- Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Amy K Y Fu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
| | - Nancy Y Ip
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China.
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China.
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Jiang Y, Zhou X, Wong HY, Ouyang L, Ip FCF, Chau VMN, Lau SF, Wu W, Wong DYK, Seo H, Fu WY, Lai NCH, Chen Y, Chen Y, Tong EPS, Mok VCT, Kwok TCY, Mok KY, Shoai M, Lehallier B, Losada PM, O'Brien E, Porter T, Laws SM, Hardy J, Wyss-Coray T, Masters CL, Fu AKY, Ip NY. An IL1RL1 genetic variant lowers soluble ST2 levels and the risk effects of APOE-ε4 in female patients with Alzheimer's disease. Nat Aging 2022; 2:616-634. [PMID: 37117777 PMCID: PMC10154240 DOI: 10.1038/s43587-022-00241-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 05/23/2022] [Indexed: 04/30/2023]
Abstract
Changes in the levels of circulating proteins are associated with Alzheimer's disease (AD), whereas their pathogenic roles in AD are unclear. Here, we identified soluble ST2 (sST2), a decoy receptor of interleukin-33-ST2 signaling, as a new disease-causing factor in AD. Increased circulating sST2 level is associated with more severe pathological changes in female individuals with AD. Genome-wide association analysis and CRISPR-Cas9 genome editing identified rs1921622 , a genetic variant in an enhancer element of IL1RL1, which downregulates gene and protein levels of sST2. Mendelian randomization analysis using genetic variants, including rs1921622 , demonstrated that decreased sST2 levels lower AD risk and related endophenotypes in females carrying the Apolipoprotein E (APOE)-ε4 genotype; the association is stronger in Chinese than in European-descent populations. Human and mouse transcriptome and immunohistochemical studies showed that rs1921622 /sST2 regulates amyloid-beta (Aβ) pathology through the modulation of microglial activation and Aβ clearance. These findings demonstrate how sST2 level is modulated by a genetic variation and plays a disease-causing role in females with AD.
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Affiliation(s)
- Yuanbing Jiang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Xiaopu Zhou
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development; Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China
| | - Hiu Yi Wong
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Li Ouyang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Fanny C F Ip
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development; Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China
| | - Vicky M N Chau
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Shun-Fat Lau
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Wei Wu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Daniel Y K Wong
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Heukjin Seo
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Wing-Yu Fu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Nicole C H Lai
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Yuewen Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development; Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China
- The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
| | - Yu Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development; Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China
- The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
| | - Estella P S Tong
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Vincent C T Mok
- Gerald Choa Neuroscience Centre, Lui Che Woo Institute of Innovative Medicine, Therese Pei Fong Chow Research Centre for Prevention of Dementia, Division of Neurology, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Timothy C Y Kwok
- Therese Pei Fong Chow Research Centre for Prevention of Dementia, Division of Geriatrics, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Kin Y Mok
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute, University College London, London, UK
| | - Maryam Shoai
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute, University College London, London, UK
| | - Benoit Lehallier
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
- Alkahest Inc, San Carlos, California, USA
| | - Patricia Morán Losada
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, California, USA
| | - Eleanor O'Brien
- Centre for Precision Health, Edith Cowan University, Joondalup, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia
| | - Simon M Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia
| | - John Hardy
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute, University College London, London, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Tony Wyss-Coray
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, California, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, California, USA
| | - Colin L Masters
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Australia
| | - Amy K Y Fu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development; Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China
| | - Nancy Y Ip
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China.
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development; Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China.
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3
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Jiang Y, Zhou X, Ip FC, Chan P, Chen Y, Lai NCH, Cheung K, Lo RMN, Tong EPS, Wong BWY, Chan ALT, Mok VCT, Kwok TCY, Mok KY, Hardy J, Zetterberg H, Fu AKY, Ip NY. Large-scale plasma proteomic profiling identifies a high-performance biomarker panel for Alzheimer's disease screening and staging. Alzheimers Dement 2021; 18:88-102. [PMID: 34032364 PMCID: PMC9292367 DOI: 10.1002/alz.12369] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/29/2021] [Accepted: 04/05/2021] [Indexed: 12/18/2022]
Abstract
Introduction Blood proteins are emerging as candidate biomarkers for Alzheimer's disease (AD). We systematically profiled the plasma proteome to identify novel AD blood biomarkers and develop a high‐performance, blood‐based test for AD. Methods We quantified 1160 plasma proteins in a Hong Kong Chinese cohort by high‐throughput proximity extension assay and validated the results in an independent cohort. In subgroup analyses, plasma biomarkers for amyloid, tau, phosphorylated tau, and neurodegeneration were used as endophenotypes of AD. Results We identified 429 proteins that were dysregulated in AD plasma. We selected 19 “hub proteins” representative of the AD plasma protein profile, which formed the basis of a scoring system that accurately classified clinical AD (area under the curve = 0.9690–0.9816) and associated endophenotypes. Moreover, specific hub proteins exhibit disease stage‐dependent dysregulation, which can delineate AD stages. Discussion This study comprehensively profiled the AD plasma proteome and serves as a foundation for a high‐performance, blood‐based test for clinical AD screening and staging.
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Affiliation(s)
- Yuanbing Jiang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiaopu Zhou
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China.,Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development; Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China
| | - Fanny C Ip
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China.,Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development; Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China
| | - Philip Chan
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yu Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China.,Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development; Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China.,The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
| | - Nicole C H Lai
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Kit Cheung
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ronnie M N Lo
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Estella P S Tong
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Bonnie W Y Wong
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Andrew L T Chan
- Divisions of Neurology and Geriatrics, Department of Medicine, Queen Elizabeth Hospital, Hong Kong, China
| | - Vincent C T Mok
- Gerald Choa Neuroscience Centre, Lui Che Woo Institute of Innovative Medicine, Therese Pei Fong Chow Research Centre for Prevention of Dementia, Division of Neurology, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Timothy C Y Kwok
- Therese Pei Fong Chow Research Centre for Prevention of Dementia, Division of Geriatrics, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Kin Y Mok
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China.,Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - John Hardy
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China.,Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Henrik Zetterberg
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China.,Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK.,UK Dementia Research Institute at UCL, London, UK.,Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Amy K Y Fu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China.,Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development; Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China
| | - Nancy Y Ip
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China.,Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development; Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China
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4
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Zhou X, Chen Y, Ip FCF, Lai NCH, Li YYT, Jiang Y, Zhong H, Chen Y, Zhang Y, Ma S, Lo RMN, Cheung K, Tong EPS, Ko H, Shoai M, Mok KY, Hardy J, Mok VCT, Kwok TCY, Fu AKY, Ip NY. Genetic and polygenic risk score analysis for Alzheimer's disease in the Chinese population. Alzheimers Dement (Amst) 2020; 12:e12074. [PMID: 32775599 PMCID: PMC7403835 DOI: 10.1002/dad2.12074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Dozens of Alzheimer's disease (AD)-associated loci have been identified in European-descent populations, but their effects have not been thoroughly investigated in the Hong Kong Chinese population. METHODS TaqMan array genotyping was performed for known AD-associated variants in a Hong Kong Chinese cohort. Regression analysis was conducted to study the associations of variants with AD-associated traits and biomarkers. Lasso regression was applied to establish a polygenic risk score (PRS) model for AD risk prediction. RESULTS SORL1 is associated with AD in the Hong Kong Chinese population. Meta-analysis corroborates the AD-protective effect of the SORL1 rs11218343 C allele. The PRS is developed and associated with AD risk, cognitive status, and AD-related endophenotypes. TREM2 H157Y might influence the amyloid beta 42/40 ratio and levels of immune-associated proteins in plasma. DISCUSSION SORL1 is associated with AD in the Hong Kong Chinese population. The PRS model can predict AD risk and cognitive status in this population.
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Affiliation(s)
- Xiaopu Zhou
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong KongChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
| | - Yu Chen
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
- The Brain Cognition and Brain Disease InstituteShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdongChina
| | - Fanny C. F. Ip
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong KongChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
| | - Nicole C. H. Lai
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Yolanda Y. T. Li
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Yuanbing Jiang
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Huan Zhong
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Yuewen Chen
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
| | - Yulin Zhang
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
| | - Shuangshuang Ma
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
| | - Ronnie M. N. Lo
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Kit Cheung
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Estella P. S. Tong
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Ho Ko
- Division of NeurologyDepartment of Medicine and TherapeuticsLi Ka Shing Institute of Health SciencesSchool of Biomedical SciencesGerald Choa Neuroscience CenterFaculty of MedicineThe Chinese University of Hong KongShatinHong KongChina
| | - Maryam Shoai
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
| | - Kin Y. Mok
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong KongChina
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
| | - John Hardy
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong KongChina
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
- Institute for Advanced StudyThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Vincent C. T. Mok
- Gerald Choa Neuroscience CentreLui Che Woo Institute of Innovative MedicineTherese Pei Fong Chow Research Centre for Prevention of DementiaDivision of NeurologyDepartment of Medicine and TherapeuticsThe Chinese University of Hong KongShatinHong KongChina
| | - Timothy C. Y. Kwok
- Therese Pei Fong Chow Research Centre for Prevention of DementiaDivision of GeriatricsDepartment of Medicine and TherapeuticsThe Chinese University of Hong KongShatinHong KongChina
| | - Amy K. Y. Fu
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong KongChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
| | - Nancy Y. Ip
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong KongChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
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