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Wei K, Qian F, Li Y, Zeng T, Huang T. Integrating multi-omics data of childhood asthma using a deep association model. FUNDAMENTAL RESEARCH 2024; 4:738-751. [PMID: 39156565 PMCID: PMC11330118 DOI: 10.1016/j.fmre.2024.03.022] [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: 06/23/2023] [Revised: 03/06/2024] [Accepted: 03/17/2024] [Indexed: 08/20/2024] Open
Abstract
Childhood asthma is one of the most common respiratory diseases with rising mortality and morbidity. The multi-omics data is providing a new chance to explore collaborative biomarkers and corresponding diagnostic models of childhood asthma. To capture the nonlinear association of multi-omics data and improve interpretability of diagnostic model, we proposed a novel deep association model (DAM) and corresponding efficient analysis framework. First, the Deep Subspace Reconstruction was used to fuse the omics data and diagnostic information, thereby correcting the distribution of the original omics data and reducing the influence of unnecessary data noises. Second, the Joint Deep Semi-Negative Matrix Factorization was applied to identify different latent sample patterns and extract biomarkers from different omics data levels. Third, our newly proposed Deep Orthogonal Canonical Correlation Analysis can rank features in the collaborative module, which are able to construct the diagnostic model considering nonlinear correlation between different omics data levels. Using DAM, we deeply analyzed the transcriptome and methylation data of childhood asthma. The effectiveness of DAM is verified from the perspectives of algorithm performance and biological significance on the independent test dataset, by ablation experiment and comparison with many baseline methods from clinical and biological studies. The DAM-induced diagnostic model can achieve a prediction AUC of 0.912, which is higher than that of many other alternative methods. Meanwhile, relevant pathways and biomarkers of childhood asthma are also recognized to be collectively altered on the gene expression and methylation levels. As an interpretable machine learning approach, DAM simultaneously considers the non-linear associations among samples and those among biological features, which should help explore interpretative biomarker candidates and efficient diagnostic models from multi-omics data analysis for human complex diseases.
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Affiliation(s)
- Kai Wei
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo 315000, China
| | - Fang Qian
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yixue Li
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Guangzhou National Laboratory, Guangzhou 510000, China
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou 510000, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Tao Zeng
- Guangzhou National Laboratory, Guangzhou 510000, China
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou 510000, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Oveisgharan S, Yang J, Yu L, Burba D, Bang W, Tasaki S, Grodstein F, Wang Y, Zhao J, De Jager PL, Schneider JA, Bennett DA. Estrogen Receptor Genes, Cognitive Decline, and Alzheimer Disease. Neurology 2023; 100:e1474-e1487. [PMID: 36697247 PMCID: PMC10104608 DOI: 10.1212/wnl.0000000000206833] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/05/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND AND OBJECTIVES Lifetime risk of Alzheimer disease (AD) dementia is twofold higher in women compared with men, and low estrogen levels in postmenopause have been suggested as a possible contributor. We examined 3 ER (GPER1, ER2, and ER1) variants in association with AD traits as an indirect method to test the association between estrogen and AD in women. Although the study focus was on women, in a comparison, we separately examined ER molecular variants in men. METHODS Participants were followed for an average of 10 years in one of the 2 longitudinal clinical pathologic studies of aging. Global cognition was assessed using a composite score derived from 19 neuropsychological tests' scores. Postmortem pathologic assessment included examination of 3 AD (amyloid-β and tau tangles determined by immunohistochemistry, and a global AD pathology score derived from diffuse and neurotic plaques and neurofibrillary tangle count) and 8 non-AD pathology indices. ER molecular genomic variants included genotyping and examining ER DNA methylation and RNA expression in brain regions including the dorsolateral prefrontal cortex (DLPFC) that are major players in cognition and often have AD pathology. RESULTS The mean age of women (N = 1711) at baseline was 78.0 (SD = 7.7) years. In women, GPER1 molecular variants had the most consistent associations with AD traits. GPER1 DNA methylation was associated with cognitive decline, tau tangle density, and global AD pathology score. GPER1 RNA expression in DLPFC was related to cognitive decline and tau tangle density. Other associations included associations of ER2 and ER1 sequence variants and DNA methylation with cognition. RNA expressions in DLPFC of genes involved in signaling mechanisms of activated ERs were also associated with cognitive decline and tau tangle density in women. In men (N = 651, average age at baseline: 77.4 [SD = 7.3]), there were less robust associations between ER molecular genomic variants and AD cognitive and pathologic traits. No consistent association was seen between ER molecular genomic variations and non-AD pathologies in either of the sexes. DISCUSSION ER DNA methylation and RNA expression, and to some extent ER polymorphisms, were associated with AD cognitive and pathologic traits in women, and to a lesser extent in men.
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Affiliation(s)
- Shahram Oveisgharan
- From the Rush Alzheimer's Disease Center (S.O., J.Y., L.Y., D.B., W.B., S.T., F.G., Y.W., J.A.S., D.A.B.), Rush University Medical Center, Chicago; Departments of Neurological Sciences (S.O., J.Y., L.Y., S.T., J.A.S., D.A.B.) and Internal Medicine (F.G.), Rush University Medical Center, Chicago, IL; Department of Epidemiology (J.Z.), University of Florida, Gainesville; Center for Translational & Computational Neuroimmunology (P.L.D.J.), Department of Neurology, Columbia University Irving Medical Center, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (P.L.D.J.), Columbia University Irving Medical Center, New York, New York; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL.
| | - Jingyun Yang
- From the Rush Alzheimer's Disease Center (S.O., J.Y., L.Y., D.B., W.B., S.T., F.G., Y.W., J.A.S., D.A.B.), Rush University Medical Center, Chicago; Departments of Neurological Sciences (S.O., J.Y., L.Y., S.T., J.A.S., D.A.B.) and Internal Medicine (F.G.), Rush University Medical Center, Chicago, IL; Department of Epidemiology (J.Z.), University of Florida, Gainesville; Center for Translational & Computational Neuroimmunology (P.L.D.J.), Department of Neurology, Columbia University Irving Medical Center, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (P.L.D.J.), Columbia University Irving Medical Center, New York, New York; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Lei Yu
- From the Rush Alzheimer's Disease Center (S.O., J.Y., L.Y., D.B., W.B., S.T., F.G., Y.W., J.A.S., D.A.B.), Rush University Medical Center, Chicago; Departments of Neurological Sciences (S.O., J.Y., L.Y., S.T., J.A.S., D.A.B.) and Internal Medicine (F.G.), Rush University Medical Center, Chicago, IL; Department of Epidemiology (J.Z.), University of Florida, Gainesville; Center for Translational & Computational Neuroimmunology (P.L.D.J.), Department of Neurology, Columbia University Irving Medical Center, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (P.L.D.J.), Columbia University Irving Medical Center, New York, New York; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Dominika Burba
- From the Rush Alzheimer's Disease Center (S.O., J.Y., L.Y., D.B., W.B., S.T., F.G., Y.W., J.A.S., D.A.B.), Rush University Medical Center, Chicago; Departments of Neurological Sciences (S.O., J.Y., L.Y., S.T., J.A.S., D.A.B.) and Internal Medicine (F.G.), Rush University Medical Center, Chicago, IL; Department of Epidemiology (J.Z.), University of Florida, Gainesville; Center for Translational & Computational Neuroimmunology (P.L.D.J.), Department of Neurology, Columbia University Irving Medical Center, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (P.L.D.J.), Columbia University Irving Medical Center, New York, New York; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Woojeong Bang
- From the Rush Alzheimer's Disease Center (S.O., J.Y., L.Y., D.B., W.B., S.T., F.G., Y.W., J.A.S., D.A.B.), Rush University Medical Center, Chicago; Departments of Neurological Sciences (S.O., J.Y., L.Y., S.T., J.A.S., D.A.B.) and Internal Medicine (F.G.), Rush University Medical Center, Chicago, IL; Department of Epidemiology (J.Z.), University of Florida, Gainesville; Center for Translational & Computational Neuroimmunology (P.L.D.J.), Department of Neurology, Columbia University Irving Medical Center, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (P.L.D.J.), Columbia University Irving Medical Center, New York, New York; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Shinya Tasaki
- From the Rush Alzheimer's Disease Center (S.O., J.Y., L.Y., D.B., W.B., S.T., F.G., Y.W., J.A.S., D.A.B.), Rush University Medical Center, Chicago; Departments of Neurological Sciences (S.O., J.Y., L.Y., S.T., J.A.S., D.A.B.) and Internal Medicine (F.G.), Rush University Medical Center, Chicago, IL; Department of Epidemiology (J.Z.), University of Florida, Gainesville; Center for Translational & Computational Neuroimmunology (P.L.D.J.), Department of Neurology, Columbia University Irving Medical Center, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (P.L.D.J.), Columbia University Irving Medical Center, New York, New York; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Fran Grodstein
- From the Rush Alzheimer's Disease Center (S.O., J.Y., L.Y., D.B., W.B., S.T., F.G., Y.W., J.A.S., D.A.B.), Rush University Medical Center, Chicago; Departments of Neurological Sciences (S.O., J.Y., L.Y., S.T., J.A.S., D.A.B.) and Internal Medicine (F.G.), Rush University Medical Center, Chicago, IL; Department of Epidemiology (J.Z.), University of Florida, Gainesville; Center for Translational & Computational Neuroimmunology (P.L.D.J.), Department of Neurology, Columbia University Irving Medical Center, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (P.L.D.J.), Columbia University Irving Medical Center, New York, New York; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Yanling Wang
- From the Rush Alzheimer's Disease Center (S.O., J.Y., L.Y., D.B., W.B., S.T., F.G., Y.W., J.A.S., D.A.B.), Rush University Medical Center, Chicago; Departments of Neurological Sciences (S.O., J.Y., L.Y., S.T., J.A.S., D.A.B.) and Internal Medicine (F.G.), Rush University Medical Center, Chicago, IL; Department of Epidemiology (J.Z.), University of Florida, Gainesville; Center for Translational & Computational Neuroimmunology (P.L.D.J.), Department of Neurology, Columbia University Irving Medical Center, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (P.L.D.J.), Columbia University Irving Medical Center, New York, New York; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Jinying Zhao
- From the Rush Alzheimer's Disease Center (S.O., J.Y., L.Y., D.B., W.B., S.T., F.G., Y.W., J.A.S., D.A.B.), Rush University Medical Center, Chicago; Departments of Neurological Sciences (S.O., J.Y., L.Y., S.T., J.A.S., D.A.B.) and Internal Medicine (F.G.), Rush University Medical Center, Chicago, IL; Department of Epidemiology (J.Z.), University of Florida, Gainesville; Center for Translational & Computational Neuroimmunology (P.L.D.J.), Department of Neurology, Columbia University Irving Medical Center, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (P.L.D.J.), Columbia University Irving Medical Center, New York, New York; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Philip Lawrence De Jager
- From the Rush Alzheimer's Disease Center (S.O., J.Y., L.Y., D.B., W.B., S.T., F.G., Y.W., J.A.S., D.A.B.), Rush University Medical Center, Chicago; Departments of Neurological Sciences (S.O., J.Y., L.Y., S.T., J.A.S., D.A.B.) and Internal Medicine (F.G.), Rush University Medical Center, Chicago, IL; Department of Epidemiology (J.Z.), University of Florida, Gainesville; Center for Translational & Computational Neuroimmunology (P.L.D.J.), Department of Neurology, Columbia University Irving Medical Center, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (P.L.D.J.), Columbia University Irving Medical Center, New York, New York; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - Julie A Schneider
- From the Rush Alzheimer's Disease Center (S.O., J.Y., L.Y., D.B., W.B., S.T., F.G., Y.W., J.A.S., D.A.B.), Rush University Medical Center, Chicago; Departments of Neurological Sciences (S.O., J.Y., L.Y., S.T., J.A.S., D.A.B.) and Internal Medicine (F.G.), Rush University Medical Center, Chicago, IL; Department of Epidemiology (J.Z.), University of Florida, Gainesville; Center for Translational & Computational Neuroimmunology (P.L.D.J.), Department of Neurology, Columbia University Irving Medical Center, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (P.L.D.J.), Columbia University Irving Medical Center, New York, New York; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
| | - David A Bennett
- From the Rush Alzheimer's Disease Center (S.O., J.Y., L.Y., D.B., W.B., S.T., F.G., Y.W., J.A.S., D.A.B.), Rush University Medical Center, Chicago; Departments of Neurological Sciences (S.O., J.Y., L.Y., S.T., J.A.S., D.A.B.) and Internal Medicine (F.G.), Rush University Medical Center, Chicago, IL; Department of Epidemiology (J.Z.), University of Florida, Gainesville; Center for Translational & Computational Neuroimmunology (P.L.D.J.), Department of Neurology, Columbia University Irving Medical Center, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (P.L.D.J.), Columbia University Irving Medical Center, New York, New York; and Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL
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