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He R, Cheng J, Qiu Y, Hu Y, Liu J, Wang TH, Cao X. IGF1R and FLT1 in female endothelial cells and CHD2 in male microglia play important roles in Alzheimer's disease based on gender difference analysis. Exp Gerontol 2024; 194:112512. [PMID: 38971545 DOI: 10.1016/j.exger.2024.112512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 06/29/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
OBJECTIVE This study investigated sex-specific pathogenesis mechanisms in Alzheimer's disease (AD) using single-nucleus RNA sequencing (snRNA-seq) data. METHODS Data from the Gene Expression Omnibus (GEO) were searched using terms "Alzheimer's Disease", "single cell", and "Homo sapiens". Studies excluding APOE E4 and including comprehensive gender information with 10× sequencing methods were selected, resulting in GSE157827 and GSE174367 datasets from human prefrontal cortex samples. Sex-stratified analyses were conducted on these datasets, and the outcomes of the analysis for GSE157827 were compared with those of GSE174367. The findings were validated using expression profiling from the mouse dataset GSE85162. Furthermore, real-time PCR experiments in mice further confirmed these findings. The Seurat R package was used to identify cell types, and batch effects were mitigated using the Harmony R package. Cell proportions by sex were compared using the Mann-Whitney-Wilcoxon test, and gene expression variability was displayed with an empirical cumulative distribution plot. Differentially expressed genes were identified using the FindMarkers function with the MAST test. Transcription factors were analyzed using the RcisTarget R package. RESULTS Seven cell types were identified: astrocytes, endothelial cells, excitatory neurons, inhibitory neurons, microglia, oligodendrocytes, and oligodendrocyte progenitor cells. Additionally, five distinct subpopulations of both endothelial and microglial cells were also identified, respectively. Key findings included: (1) In endothelial cells, genes involved in synapse organization, such as Insulin Like Growth Factor 1 Receptor (IGF1R) and Fms Related Receptor Tyrosine Kinase 1(FLT1), showed higher expression in females with AD. (2) In microglial cells, genes in the ribosome pathway exhibited higher expression in males without AD compared to females (with or without AD) and males with AD. (3) Chromodomain Helicase DNA Binding Protein 2 (CHD2) negatively regulated gene expression in the ribosome pathway in male microglia, suppressing AD, this finding was further validated in mice. (4) Differences between Asians and Caucasians were observed based on sex and disease status stratification. CONCLUSIONS IGF1R and FLT1 in endothelial cells contribute to AD in females, while CHD2 negatively regulates ribosome pathway gene expression in male microglia, suppressing AD in humans and mice.
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Affiliation(s)
- Rong He
- Laboratory Animal Department, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Jishuai Cheng
- Laboratory Animal Department, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Yue Qiu
- Dermatology Department of Xiangya Hospital, Central South University, Changsha, China
| | - Yiwen Hu
- Laboratory Animal Department, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Jia Liu
- Laboratory Animal Department, Kunming Medical University, Kunming 650500, Yunnan, China.
| | - Ting-Hua Wang
- Laboratory Animal Department, Kunming Medical University, Kunming 650500, Yunnan, China.
| | - Xue Cao
- Laboratory Animal Department, Kunming Medical University, Kunming 650500, Yunnan, China.
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2
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Heuer SE, Bloss EB, Howell GR. Strategies to dissect microglia-synaptic interactions during aging and in Alzheimer's disease. Neuropharmacology 2024; 254:109987. [PMID: 38705570 DOI: 10.1016/j.neuropharm.2024.109987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Age is the largest risk factor for developing Alzheimer's disease (AD), a neurodegenerative disorder that causes a progressive and severe dementia. The underlying cause of cognitive deficits seen in AD is thought to be the disconnection of neural circuits that control memory and executive functions. Insight into the mechanisms by which AD diverges from normal aging will require identifying precisely which cellular events are driven by aging and which are impacted by AD-related pathologies. Since microglia, the brain-resident macrophages, are known to have critical roles in the formation and maintenance of neural circuits through synaptic pruning, they are well-positioned to modulate synaptic connectivity in circuits sensitive to aging or AD. In this review, we provide an overview of the current state of the field and on emerging technologies being employed to elucidate microglia-synaptic interactions in aging and AD. We also discuss the importance of leveraging genetic diversity to study how these interactions are shaped across more realistic contexts. We propose that these approaches will be essential to define specific aging- and disease-relevant trajectories for more personalized therapeutics aimed at reducing the effects of age or AD pathologies on the brain. This article is part of the Special Issue on "Microglia".
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Affiliation(s)
- Sarah E Heuer
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA; Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Erik B Bloss
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA; Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, 02111, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, 04469, USA.
| | - Gareth R Howell
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA; Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, 02111, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, 04469, USA.
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3
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Liao Z, Zhang Q, Ren N, Zhao H, Zheng X. Progress in mitochondrial and omics studies in Alzheimer's disease research: from molecular mechanisms to therapeutic interventions. Front Immunol 2024; 15:1418939. [PMID: 39040111 PMCID: PMC11260616 DOI: 10.3389/fimmu.2024.1418939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/21/2024] [Indexed: 07/24/2024] Open
Abstract
Alzheimer's disease (Alzheimer's disease, AD) is a progressive neurological disorder characterized by memory loss and cognitive impairment. It is characterized by the formation of tau protein neurofibrillary tangles and β-amyloid plaques. Recent studies have found that mitochondria in neuronal cells of AD patients exhibit various dysfunctions, including reduced numbers, ultrastructural changes, reduced enzyme activity, and abnormal kinetics. These abnormal mitochondria not only lead to the loss of normal neuronal cell function, but are also a major driver of AD progression. In this review, we will focus on the advances of mitochondria and their multi-omics in AD research, with particular emphasis on how mitochondrial dysfunction in AD drives disease progression. At the same time, we will focus on summarizing how mitochondrial genomics technologies have revealed specific details of these dysfunctions and how therapeutic strategies targeting mitochondria may provide new directions for future AD treatments. By delving into the key mechanisms of mitochondria in AD related to energy metabolism, altered kinetics, regulation of cell death, and dysregulation of calcium-ion homeostasis, and how mitochondrial multi-omics technologies can be utilized to provide us with a better understanding of these processes. In the future, mitochondria-centered therapeutic strategies will be a key idea in the treatment of AD.
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Affiliation(s)
- Zuning Liao
- Department of Neurology, Fourth People’s Hospital of Jinan, Jinan, China
| | - Qiying Zhang
- Department of Internal Medicine, Jinan Municipal Government Hospital, Jinan, China
| | - Na Ren
- Pharmacy Department, Jinan Municipal People’s Government Organs Outpatient Department, Jinan, China
| | - Haiyan Zhao
- Department of Pharmacy, Qihe County People’s Hospital, Dezhou, China
| | - Xueyan Zheng
- Department of Pharmacy, Jinan Second People’s Hospital, Jinan, China
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4
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Tang AS, Woldemariam SR, Miramontes S, Norgeot B, Oskotsky TT, Sirota M. Harnessing EHR data for health research. Nat Med 2024; 30:1847-1855. [PMID: 38965433 DOI: 10.1038/s41591-024-03074-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 05/17/2024] [Indexed: 07/06/2024]
Abstract
With the increasing availability of rich, longitudinal, real-world clinical data recorded in electronic health records (EHRs) for millions of patients, there is a growing interest in leveraging these records to improve the understanding of human health and disease and translate these insights into clinical applications. However, there is also a need to consider the limitations of these data due to various biases and to understand the impact of missing information. Recognizing and addressing these limitations can inform the design and interpretation of EHR-based informatics studies that avoid confusing or incorrect conclusions, particularly when applied to population or precision medicine. Here we discuss key considerations in the design, implementation and interpretation of EHR-based informatics studies, drawing from examples in the literature across hypothesis generation, hypothesis testing and machine learning applications. We outline the growing opportunities for EHR-based informatics studies, including association studies and predictive modeling, enabled by evolving AI capabilities-while addressing limitations and potential pitfalls to avoid.
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Affiliation(s)
- Alice S Tang
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Sarah R Woldemariam
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Silvia Miramontes
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | | | - Tomiko T Oskotsky
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
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5
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Miramontes S, Pereda Serras C, Woldemariam SR, Khan U, Li Y, Tang AS, Tsoy E, Oskotsky TT, Sirota M. Alzheimer's disease as a women's health challenge: a call for action on integrative precision medicine approaches. NPJ WOMEN'S HEALTH 2024; 2:17. [PMID: 38778871 PMCID: PMC11106001 DOI: 10.1038/s44294-024-00021-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Alzheimer's Disease (AD) is marked by pronounced sex differences in pathophysiology and progression. However, the field has yet to fully recognize AD as a women's health issue, delaying the development of targeted preventative strategies and treatments. This perspective explores the elements impacting AD in women, identifying sex specificity in risk factors, highlighting new diagnostic approaches with electronic health records, and reviewing key molecular studies to underscore the need for integrative precision medicine approaches. Established AD risk factors such as advancing age, the apolipoprotein E4 allele, and poorer cardiovascular health affect women differently. We also shed light on sociocultural risk factors, focusing on the gender disparities that may play a role in AD development. From a biological perspective, sex differences in AD are apparent in biomarkers and transcriptomics, further emphasizing the need for targeted diagnostics and treatments. The convergence of novel multiomics data and cutting-edge computational tools provides a unique opportunity to study the molecular underpinnings behind sex dimorphism in AD. Thus, precision medicine emerges as a promising framework for understanding AD pathogenesis through the integration of genetics, sex, environment, and lifestyle. By characterizing AD as a women's health challenge, we can catalyze a transformative shift in AD research and care, marked by improved diagnostic accuracy, targeted interventions, and ultimately, enhanced clinical outcomes.
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Affiliation(s)
- S. Miramontes
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA USA
| | - C. Pereda Serras
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA USA
| | - S. R. Woldemariam
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA USA
| | - U. Khan
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA USA
| | - Y. Li
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA USA
| | - A. S. Tang
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA USA
| | - E. Tsoy
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA USA
- Global Brain Health Institute, University of California San Francisco, San Francisco, CA USA
| | - T. T. Oskotsky
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA USA
| | - M. Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA USA
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6
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Ramey GD, Tang A, Phongpreecha T, Yang MM, Woldemariam SR, Oskotsky TT, Montine TJ, Allen I, Miller ZA, Aghaeepour N, Capra JA, Sirota M. Exposure to autoimmune disorders increases Alzheimer's disease risk in a multi-site electronic health record analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.02.24306649. [PMID: 38746318 PMCID: PMC11092711 DOI: 10.1101/2024.05.02.24306649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Molecular studies of Alzheimer's disease (AD) implicate potential links between autoimmunity and AD, but the underlying clinical relationships between these conditions remain poorly understood. Electronic health records (EHRs) provide an opportunity to determine the clinical risk relationship between autoimmune disorders and AD and understand whether specific disorders and disorder subtypes affect AD risk at the phenotypic level in human populations. We evaluated relationships between 26 autoimmune disorders and AD across retrospective observational case-control and cohort study designs in the EHR systems at UCSF and Stanford. We quantified overall and sex-specific AD risk effects that these autoimmune disorders confer. We identified significantly increased AD risk in autoimmune disorder patients in both study designs at UCSF and at Stanford. This pattern was driven by specific autoimmunity subtypes including endocrine, gastrointestinal, dermatologic, and musculoskeletal disorders. We also observed increased AD risk from autoimmunity in both women and men, but women with autoimmune disorders continued to have a higher AD prevalence than men, indicating persistent sex-specificity. This study identifies autoimmune disorders as strong risk factors for AD that validate across several study designs and EHR databases. It sets the foundation for exploring how underlying autoimmune mechanisms increase AD risk and contribute to AD pathogenesis.
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7
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Adewale Q, Khan AF, Bennett DA, Iturria-Medina Y. Single-nucleus RNA velocity reveals critical synaptic and cell-cycle dysregulations in neuropathologically confirmed Alzheimer's disease. Sci Rep 2024; 14:7269. [PMID: 38538816 PMCID: PMC10973452 DOI: 10.1038/s41598-024-57918-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024] Open
Abstract
Typical differential single-nucleus gene expression (snRNA-seq) analyses in Alzheimer's disease (AD) provide fixed snapshots of cellular alterations, making the accurate detection of temporal cell changes challenging. To characterize the dynamic cellular and transcriptomic differences in AD neuropathology, we apply the novel concept of RNA velocity to the study of single-nucleus RNA from the cortex of 60 subjects with varied levels of AD pathology. RNA velocity captures the rate of change of gene expression by comparing intronic and exonic sequence counts. We performed differential analyses to find the significant genes driving both cell type-specific RNA velocity and expression differences in AD, extensively compared these two transcriptomic metrics, and clarified their associations with multiple neuropathologic traits. The results were cross-validated in an independent dataset. Comparison of AD pathology-associated RNA velocity with parallel gene expression differences reveals sets of genes and molecular pathways that underlie the dynamic and static regimes of cell type-specific dysregulations underlying the disease. Differential RNA velocity and its linked progressive neuropathology point to significant dysregulations in synaptic organization and cell development across cell types. Notably, most of the genes underlying this synaptic dysregulation showed increased RNA velocity in AD subjects compared to controls. Accelerated cell changes were also observed in the AD subjects, suggesting that the precocious depletion of precursor cell pools might be associated with neurodegeneration. Overall, this study uncovers active molecular drivers of the spatiotemporal alterations in AD and offers novel insights towards gene- and cell-centric therapeutic strategies accounting for dynamic cell perturbations and synaptic disruptions.
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Affiliation(s)
- Quadri Adewale
- Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill University, Y I-M, 3801 University Street, Room NW312, Montreal, H3A 2B4, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Canada
| | - Ahmed F Khan
- Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill University, Y I-M, 3801 University Street, Room NW312, Montreal, H3A 2B4, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Canada
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Yasser Iturria-Medina
- Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill University, Y I-M, 3801 University Street, Room NW312, Montreal, H3A 2B4, Canada.
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada.
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Canada.
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8
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Tang AS, Rankin KP, Cerono G, Miramontes S, Mills H, Roger J, Zeng B, Nelson C, Soman K, Woldemariam S, Li Y, Lee A, Bove R, Glymour M, Aghaeepour N, Oskotsky TT, Miller Z, Allen IE, Sanders SJ, Baranzini S, Sirota M. Leveraging electronic health records and knowledge networks for Alzheimer's disease prediction and sex-specific biological insights. NATURE AGING 2024; 4:379-395. [PMID: 38383858 PMCID: PMC10950787 DOI: 10.1038/s43587-024-00573-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024]
Abstract
Identification of Alzheimer's disease (AD) onset risk can facilitate interventions before irreversible disease progression. We demonstrate that electronic health records from the University of California, San Francisco, followed by knowledge networks (for example, SPOKE) allow for (1) prediction of AD onset and (2) prioritization of biological hypotheses, and (3) contextualization of sex dimorphism. We trained random forest models and predicted AD onset on a cohort of 749 individuals with AD and 250,545 controls with a mean area under the receiver operating characteristic of 0.72 (7 years prior) to 0.81 (1 day prior). We further harnessed matched cohort models to identify conditions with predictive power before AD onset. Knowledge networks highlight shared genes between multiple top predictors and AD (for example, APOE, ACTB, IL6 and INS). Genetic colocalization analysis supports AD association with hyperlipidemia at the APOE locus, as well as a stronger female AD association with osteoporosis at a locus near MS4A6A. We therefore show how clinical data can be utilized for early AD prediction and identification of personalized biological hypotheses.
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Affiliation(s)
- Alice S Tang
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Graduate Program in Bioengineering, University of California, San Francisco and University of California, Berkeley, San Francisco and Berkeley, CA, USA.
| | - Katherine P Rankin
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Gabriel Cerono
- Weill Institute for Neuroscience. Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Silvia Miramontes
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Hunter Mills
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Jacquelyn Roger
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Billy Zeng
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Charlotte Nelson
- Weill Institute for Neuroscience. Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Karthik Soman
- Weill Institute for Neuroscience. Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Sarah Woldemariam
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Yaqiao Li
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Albert Lee
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Riley Bove
- Weill Institute for Neuroscience. Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Maria Glymour
- Department of Anesthesiology, Pain, and Perioperative Medicine, Stanford University, Palo Alto, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Pain, and Perioperative Medicine, Stanford University, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University, Palo Alto, CA, USA
| | - Tomiko T Oskotsky
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Zachary Miller
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Isabel E Allen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Stephan J Sanders
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Sergio Baranzini
- Weill Institute for Neuroscience. Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Department of Pediatrics, University of California, San Francisco, CA, USA.
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9
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Han Y, Huang C, Pan Y, Gu X. Single Cell Sequencing Technology and Its Application in Alzheimer's Disease. J Alzheimers Dis 2024; 97:1033-1050. [PMID: 38217599 DOI: 10.3233/jad-230861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
Alzheimer's disease (AD) involves degeneration of cells in the brain. Due to insidious onset and slow progression, AD is often not diagnosed until it gets progressed to a more severe stage. The diagnosis and treatment of AD has been a challenge. In recent years, high-throughput sequencing technologies have exhibited advantages in exploring the pathogenesis of diseases. However, the types of cells of the central nervous system are complex and traditional bulk sequencing cannot reflect their heterogeneity. Single-cell sequencing technology enables study at the individual cell level and has an irreplaceable advantage in the study of complex diseases. In recent years, this field has expanded rapidly and several types of single-cell sequencing technologies have emerged, including transcriptomics, epigenomics, genomics and proteomics. This review article provides an overview of these single-cell sequencing technologies and their application in AD.
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Affiliation(s)
- Yuru Han
- Shanghai Key Laboratory of Molecular Imaging, Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, China
- School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Congying Huang
- Shanghai Key Laboratory of Molecular Imaging, Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, China
- School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yuhui Pan
- Center for Disease Control and Prevention of Harbin, Harbin, China
| | - Xuefeng Gu
- Shanghai Key Laboratory of Molecular Imaging, Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, China
- School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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10
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Teefy BB, Lemus AJJ, Adler A, Xu A, Bhala R, Hsu K, Benayoun BA. Widespread sex dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues. Cell Rep 2023; 42:113237. [PMID: 37837621 PMCID: PMC10842523 DOI: 10.1016/j.celrep.2023.113237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/18/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023] Open
Abstract
The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism for aging research. Here, we describe a multitissue, single-cell gene expression atlas of female and male blood, kidney, liver, and spleen. We annotate 22 cell types, define marker genes, and infer differentiation trajectories. We find pervasive sex-dimorphic gene expression across cell types. Sex-dimorphic genes tend to be linked to lipid metabolism, consistent with clear differences in lipid storage in female vs. male turquoise killifish livers. We use machine learning to predict sex using single-cell gene expression and identify potential markers for molecular sex identity. As a proof of principle, we show that our atlas can be used to deconvolute existing bulk RNA sequencing (RNA-seq) data to obtain accurate estimates of cell type proportions. This atlas can be a resource to the community that could be leveraged to develop cell-type-specific expression in transgenic animals.
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Affiliation(s)
- Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Aaron J J Lemus
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan Xu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Rajyk Bhala
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Katelyn Hsu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA; Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA; Epigenetics and Gene Regulation, USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA; USC Stem Cell Initiative, Los Angeles, CA 90089, USA.
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11
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Wingo AP, Liu Y, Gerasimov ES, Vattathil SM, Liu J, Cutler DJ, Epstein MP, Blokland GAM, Thambisetty M, Troncoso JC, Duong DM, Bennett DA, Levey AI, Seyfried NT, Wingo TS. Sex differences in brain protein expression and disease. Nat Med 2023; 29:2224-2232. [PMID: 37653343 PMCID: PMC10504083 DOI: 10.1038/s41591-023-02509-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
Most complex human traits differ by sex, but we have limited insight into the underlying mechanisms. Here, we investigated the influence of biological sex on protein expression and its genetic regulation in 1,277 human brain proteomes. We found that 13.2% (1,354) of brain proteins had sex-differentiated abundance and 1.5% (150) of proteins had sex-biased protein quantitative trait loci (sb-pQTLs). Among genes with sex-biased expression, we found 67% concordance between sex-differentiated protein and transcript levels; however, sex effects on the genetic regulation of expression were more evident at the protein level. Considering 24 psychiatric, neurologic and brain morphologic traits, we found that an average of 25% of their putatively causal genes had sex-differentiated protein abundance and 12 putatively causal proteins had sb-pQTLs. Furthermore, integrating sex-specific pQTLs with sex-stratified genome-wide association studies of six psychiatric and neurologic conditions, we uncovered another 23 proteins contributing to these traits in one sex but not the other. Together, these findings begin to provide insights into mechanisms underlying sex differences in brain protein expression and disease.
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Affiliation(s)
- Aliza P Wingo
- Veterans Affairs Atlanta Health Care System, Decatur, GA, USA.
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA.
| | - Yue Liu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Selina M Vattathil
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jiaqi Liu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Gabriëlla A M Blokland
- Department of Psychiatry and Neuropsychology, Maastricht University School for Mental Health and Neuroscience, Maastricht, the Netherlands
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas S Wingo
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
- Goizueta Alzheimer's Disease Center, Emory University School of Medicine, Atlanta, GA, USA.
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12
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Abdullatef S, Farina C. Publicly available ex vivo transcriptomics datasets to explore CNS physiology and neurodegeneration: state of the art and perspectives. Front Neurosci 2023; 17:1211079. [PMID: 37680966 PMCID: PMC10481165 DOI: 10.3389/fnins.2023.1211079] [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: 04/24/2023] [Accepted: 08/08/2023] [Indexed: 09/09/2023] Open
Abstract
The central nervous system (CNS) is characterized by an intricate composition of diverse cell types, including neurons and glia cells (astrocytes, oligodendrocytes, and microglia), whose functions may differ along time, between sexes and upon pathology. The advancements in high-throughput transcriptomics are providing fundamental insights on cell phenotypes, so that molecular codes and instructions are ever more described for CNS physiology and neurodegeneration. To facilitate the search of relevant information, this review provides an overview of key CNS transcriptomics studies ranging from CNS development to ageing and from physiology to pathology as defined for five neurodegenerative disorders and their relative animal models, with a focus on molecular descriptions whose raw data were publicly available. Accurate phenotypic descriptions of cellular states correlate with functional changes and this knowledge may support research devoted to the development of therapeutic strategies supporting CNS repair and function.
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Affiliation(s)
- Sandra Abdullatef
- Division of Neuroscience, Institute of Experimental Neurology (INSpe), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Faculty of Medicine, Università Vita-Salute San Raffaele, Milan, Italy
| | - Cinthia Farina
- Division of Neuroscience, Institute of Experimental Neurology (INSpe), IRCCS San Raffaele Scientific Institute, Milan, Italy
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13
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Walter TJ, Suter RK, Ayad NG. An overview of human single-cell RNA sequencing studies in neurobiological disease. Neurobiol Dis 2023; 184:106201. [PMID: 37321420 PMCID: PMC10470823 DOI: 10.1016/j.nbd.2023.106201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/09/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023] Open
Abstract
Neurobiological disorders are highly prevalent medical conditions that contribute to significant morbidity and mortality. Single-cell RNA sequencing (scRNA-seq) is a technique that measures gene expression in individual cells. In this review, we survey scRNA-seq studies of tissues from patients suffering from neurobiological disease. This includes postmortem human brains and organoids derived from peripheral cells. We highlight a range of conditions, including epilepsy, cognitive disorders, substance use disorders, and mood disorders. These findings provide new insights into neurobiological disease in multiple ways, including discovering novel cell types or subtypes involved in disease, proposing new pathophysiological mechanisms, uncovering novel drug targets, or identifying potential biomarkers. We discuss the quality of these findings and suggest potential future directions and areas open for additional research, including studies of non-cortical brain regions and additional conditions such as anxiety disorders, mood disorders, and sleeping disorders. We argue that additional scRNA-seq of tissues from patients suffering from neurobiological disease could advance our understanding and treatment of these conditions.
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Affiliation(s)
- T Jordan Walter
- Georgetown University, Lombardi Comprehensive Cancer Center, 3970 Reservoir Rd NW, Washington D.C. 20007, USA.
| | - Robert K Suter
- Georgetown University, Lombardi Comprehensive Cancer Center, 3970 Reservoir Rd NW, Washington D.C. 20007, USA
| | - Nagi G Ayad
- Georgetown University, Lombardi Comprehensive Cancer Center, 3970 Reservoir Rd NW, Washington D.C. 20007, USA
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14
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Hou X, Zhang X, Zou H, Guan M, Fu C, Wang W, Zhang ZR, Geng Y, Chen Y. Differential and substrate-specific inhibition of γ-secretase by the C-terminal region of ApoE2, ApoE3, and ApoE4. Neuron 2023; 111:1898-1913.e5. [PMID: 37040764 DOI: 10.1016/j.neuron.2023.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 01/16/2023] [Accepted: 03/17/2023] [Indexed: 04/13/2023]
Abstract
Aberrant low γ-secretase activity is associated with most of the presenilin mutations that underlie familial Alzheimer's disease (fAD). However, the role of γ-secretase in the more prevalent sporadic AD (sAD) remains unaddressed. Here, we report that human apolipoprotein E (ApoE), the most important genetic risk factor of sAD, interacts with γ-secretase and inhibits it with substrate specificity in cell-autonomous manners through its conserved C-terminal region (CT). This ApoE CT-mediated inhibitory activity is differentially compromised in different ApoE isoforms, resulting in an ApoE2 > ApoE3 > ApoE4 potency rank order inversely correlating to their associated AD risk. Interestingly, in an AD mouse model, neuronal ApoE CT migrates to amyloid plaques in the subiculum from other regions and alleviates the plaque burden. Together, our data reveal a hidden role of ApoE as a γ-secretase inhibitor with substrate specificity and suggest that this precision γ-inhibition by ApoE may protect against the risk of sAD.
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Affiliation(s)
- Xianglong Hou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuexin Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Zou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingfeng Guan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaoying Fu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China
| | - Wenyuan Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China
| | - Zai-Rong Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China
| | - Yang Geng
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China.
| | - Yelin Chen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Rd., B13, Pudongxinqu, Shanghai 201210, China.
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15
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Anderson AG, Rogers BB, Loupe JM, Rodriguez-Nunez I, Roberts SC, White LM, Brazell JN, Bunney WE, Bunney BG, Watson SJ, Cochran JN, Myers RM, Rizzardi LF. Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer's disease-specific cis-regulatory elements. CELL GENOMICS 2023; 3:100263. [PMID: 36950385 PMCID: PMC10025452 DOI: 10.1016/j.xgen.2023.100263] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/06/2022] [Accepted: 01/12/2023] [Indexed: 02/05/2023]
Abstract
Cell type-specific transcriptional differences between brain tissues from donors with Alzheimer's disease (AD) and unaffected controls have been well documented, but few studies have rigorously interrogated the regulatory mechanisms responsible for these alterations. We performed single nucleus multiomics (snRNA-seq plus snATAC-seq) on 105,332 nuclei isolated from cortical tissues from 7 AD and 8 unaffected donors to identify candidate cis-regulatory elements (CREs) involved in AD-associated transcriptional changes. We detected 319,861 significant correlations, or links, between gene expression and cell type-specific transposase accessible regions enriched for active CREs. Among these, 40,831 were unique to AD tissues. Validation experiments confirmed the activity of many regions, including several candidate regulators of APP expression. We identified ZEB1 and MAFB as candidate transcription factors playing important roles in AD-specific gene regulation in neurons and microglia, respectively. Microglia links were globally enriched for heritability of AD risk and previously identified active regulatory regions.
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Affiliation(s)
| | - Brianne B. Rogers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jacob M. Loupe
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Lauren M. White
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - William E. Bunney
- Department of Psychiatry and Human Behavior, College of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Blynn G. Bunney
- Department of Psychiatry and Human Behavior, College of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Stanley J. Watson
- Mental Health Research Institute, University of Michigan, Ann Arbor, MI, USA
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16
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Cui SS, Jiang QW, Chen SD. Sex difference in biological change and mechanism of Alzheimer’s disease: from macro- to micro-landscape. Ageing Res Rev 2023; 87:101918. [PMID: 36967089 DOI: 10.1016/j.arr.2023.101918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 02/16/2023] [Accepted: 03/23/2023] [Indexed: 04/05/2023]
Abstract
Alzheimer's disease (AD) is the most common form of dementia and numerous studies reported a higher prevalence and incidence of AD among women. Although women have longer lifetime, longevity does not wholly explain the higher frequency and lifetime risk in women. It is important to understand sex differences in AD pathophysiology and pathogenesis, which could provide foundation for future clinical AD research. Here, we reviewed the most recent and relevant literature on sex differences in biological change of AD from macroscopical neuroimaging to microscopical pathologic change (neuronal degeneration, synaptic dysfunction, amyloid-beta and tau accumulation). We also discussed sex differences in cellular mechanisms related to AD (neuroinflammation, mitochondria dysfunction, oxygen stress, apoptosis, autophagy, blood-brain-barrier dysfunction, gut microbiome alteration, bulk and single cell/nucleus omics) and possible causes underlying these differences including sex-chromosome, sex hormone and hypothalamic-pituitary- adrenal (HPA) axis effects.
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Affiliation(s)
- Shi-Shuang Cui
- Department of Neurology & Institute of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Geriatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qian-Wen Jiang
- Department of Neurology & Institute of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Geriatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Sheng-Di Chen
- Department of Neurology & Institute of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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17
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Santiago JA, Quinn JP, Potashkin JA. Sex-specific transcriptional rewiring in the brain of Alzheimer’s disease patients. Front Aging Neurosci 2022; 14:1009368. [PMID: 36389068 PMCID: PMC9659968 DOI: 10.3389/fnagi.2022.1009368] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/11/2022] [Indexed: 11/28/2022] Open
Abstract
Sex-specific differences may contribute to Alzheimer’s disease (AD) development. AD is more prevalent in women worldwide, and female sex has been suggested as a disease risk factor. Nevertheless, the molecular mechanisms underlying sex-biased differences in AD remain poorly characterized. To this end, we analyzed the transcriptional changes in the entorhinal cortex of symptomatic and asymptomatic AD patients stratified by sex. Co-expression network analysis implemented by SWItchMiner software identified sex-specific signatures of switch genes responsible for drastic transcriptional changes in the brain of AD and asymptomatic AD individuals. Pathway analysis of the switch genes revealed that morphine addiction, retrograde endocannabinoid signaling, and autophagy are associated with both females with AD (F-AD) and males with (M-AD). In contrast, nicotine addiction, cell adhesion molecules, oxytocin signaling, adipocytokine signaling, prolactin signaling, and alcoholism are uniquely associated with M-AD. Similarly, some of the unique pathways associated with F-AD switch genes are viral myocarditis, Hippo signaling pathway, endometrial cancer, insulin signaling, and PI3K-AKT signaling. Together these results reveal that there are many sex-specific pathways that may lead to AD. Approximately 20–30% of the elderly have an accumulation of amyloid beta in the brain, but show no cognitive deficit. Asymptomatic females (F-asymAD) and males (M-asymAD) both shared dysregulation of endocytosis. In contrast, pathways uniquely associated with F-asymAD switch genes are insulin secretion, progesterone-mediated oocyte maturation, axon guidance, renal cell carcinoma, and ErbB signaling pathway. Similarly, pathways uniquely associated with M-asymAD switch genes are fluid shear stress and atherosclerosis, FcγR mediated phagocytosis, and proteoglycans in cancer. These results reveal for the first time unique pathways associated with either disease progression or cognitive resilience in asymptomatic individuals. Additionally, we identified numerous sex-specific transcription factors and potential neurotoxic chemicals that may be involved in the pathogenesis of AD. Together these results reveal likely molecular drivers of sex differences in the brain of AD patients. Future molecular studies dissecting the functional role of these switch genes in driving sex differences in AD are warranted.
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Affiliation(s)
| | | | - Judith A. Potashkin
- Cellular and Molecular Pharmacology Department, Center for Neurodegenerative Diseases and Therapeutics, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
- *Correspondence: Judith A. Potashkin,
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18
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Herrera M, Keynan Y, McLaren PJ, Isaza JP, Abrenica B, López L, Marin D, Rueda ZV. Gene expression profiling identifies candidate biomarkers for new latent tuberculosis infections. A cohort study. PLoS One 2022; 17:e0274257. [PMID: 36170228 PMCID: PMC9518923 DOI: 10.1371/journal.pone.0274257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/25/2022] [Indexed: 11/25/2022] Open
Abstract
Objective To determine the gene expression profile in individuals with new latent tuberculosis infection (LTBI), and to compare them with people with active tuberculosis (TB) and those exposed to TB but not infected. Design A prospective cohort study. Recruitment and follow-up were conducted between September 2016 to December 2018. Gene expression and data processing and analysis from April 2019 to April 2021. Setting Two male Colombian prisons. Participants 15 new tuberculin skin test (TST) converters (negative TST at baseline that became positive during follow-up), 11 people that continued with a negative TST after two years of follow-up, and 10 people with pulmonary ATB. Main outcome measures Gene expression profile using RNA sequencing from PBMC samples. The differential expression was assessed using the DESeq2 package in Bioconductor. Genes with |logFC| >1.0 and an adjusted p-value < 0.1 were differentially expressed. We analyzed the differences in the enrichment of KEGG pathways in each group using InterMiner. Results The gene expression was affected by the time of incarceration. We identified group-specific differentially expressed genes between the groups: 289 genes in people with a new LTBI and short incarceration (less than three months of incarceration), 117 in those with LTBI and long incarceration (one or more years of incarceration), 26 in ATB, and 276 in the exposed but non-infected individuals. Four pathways encompassed the largest number of down and up-regulated genes among individuals with LTBI and short incarceration: cytokine signaling, signal transduction, neutrophil degranulation, and innate immune system. In individuals with LTBI and long incarceration, the only enriched pathway within up-regulated genes was Emi1 phosphorylation. Conclusions Recent infection with MTB is associated with an identifiable RNA pattern related to innate immune system pathways that can be used to prioritize LTBI treatment for those at greatest risk for developing active TB.
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Affiliation(s)
- Mariana Herrera
- Departments of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Doctorado en Epidemiologia, Facultad Nacional de Salud Pública, Universidad de Antioquia, Medellín, Colombia
| | - Yoav Keynan
- Departments of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Canada
- Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Paul J. McLaren
- Departments of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, Canada
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Juan Pablo Isaza
- Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Bernard Abrenica
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Lucelly López
- Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Diana Marin
- Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Zulma Vanessa Rueda
- Departments of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Colombia
- * E-mail:
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19
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Brown CM, Wong Q, Thakur A, Singh K, Singh RS. Origin of Sex-Biased Mental Disorders: Do Males and Females Experience Different Selective Regimes? J Mol Evol 2022; 90:401-417. [PMID: 36097083 DOI: 10.1007/s00239-022-10072-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/26/2022] [Indexed: 12/24/2022]
Abstract
The origins of sex-biased differences in disease and health are of growing interest to both medical researchers and health professionals. Several major factors have been identified that affect sex differences in incidence of diseases and mental disorders. These are: sex chromosomes, sex hormones and female immunity, sexual selection and antagonistic evolution, and differential susceptibility of sexes to environmental factors. These factors work on different time scales and are not exclusive of each other. Recently, a combined Sexual Selection-Sex Hormones (SS-SH) Theory was presented as an evolutionary mechanism to explain sex-biased differences in diseases and mental disorders (Singh in J Mol Evol 89:195-213, 2021). In that paper disease prevalence trends were investigated, and non-sex-specific diseases were hypothesized to be more common in males than in females in general. They showed signs of exceptions to this trend with inflammatory diseases and stress-related mental disorders that were more common in females. We believe that the SS-SH theory requires the consideration of psycho-social stress (PSS) to explain the predominance of female-biased mental disorders and some other exceptions in their findings. Here we present a theory of sex-differential experience of PSS and provide quantitative support for the combined SS-SH-PSS Theory using age-standardized incidence rates (ASIRs) recording the levels of male- and female-bias in data obtained from different countries. The grand theory provides an evolutionary framework for explaining patterns of sex-biased trends in the prevalence of disease and health. Further exploration of women's vulnerability to social factors may help to facilitate new treatments for female-biased diseases.
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Affiliation(s)
| | - Queenie Wong
- Department of Biology, McMaster University, Hamilton, Canada
| | - Aditi Thakur
- Department of Biology, McMaster University, Hamilton, Canada
| | - Karun Singh
- Krembil Research Institute, University Health Network and Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Rama S Singh
- Department of Biology, McMaster University, Hamilton, Canada.
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20
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Milner TA, Chen RX, Welington D, Rubin BR, Contoreggi NH, Johnson MA, Mazid S, Marques-Lopes J, Marongiu R, Glass MJ. Angiotensin II differentially affects hippocampal glial inflammatory markers in young adult male and female mice. Learn Mem 2022; 29:265-273. [PMID: 36206386 PMCID: PMC9488028 DOI: 10.1101/lm.053507.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/03/2022] [Indexed: 12/16/2022]
Abstract
Hypertension is a risk factor for neurodegenerative disorders involving inflammation and inflammatory cytokine-producing brain cells (microglia and astrocytes) in the hippocampus and medial prefrontal cortex (mPFC). Here we investigated the effect of slow-pressor angiotensin II (AngII) on gliosis in the hippocampus and mPFC of young adult (2-mo-old) male and female mice. In males, AngII induced hypertension, and this resulted in an increase in the density of the astrocyte marker glial fibrillary acidic protein (GFAP) in the subgranular hilus and a decrease in the density of the microglial marker ionized calcium binding adapter molecule (Iba-1) in the CA1 region. Females infused with AngII did not show hypertension but, significantly, showed alterations in hippocampal glial activation. Compared with vehicle, AngII-infused female mice had an increased density of Iba-1 in the dentate gyrus and CA2/3a region. Like males, females infused with AngII exhibited decreased Iba-1 in the CA1 region. Neither male nor female mice showed differences in GFAP or Iba-1 in the mPFC following AngII infusion. These results demonstrate that the hippocampus is particularly vulnerable to AngII in young adulthood. Differences in gonadal hormones or the sensitivity to AngII hypertension may account for divergences in GFAP and Iba-1 in males and females.
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Affiliation(s)
- Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
- Harold and Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, New York 10065, USA
| | - Ryan X Chen
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
| | - Diedreanna Welington
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
| | - Batsheva R Rubin
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
| | - Natalina H Contoreggi
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
| | - Megan A Johnson
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
| | - Sanoara Mazid
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
| | - Jose Marques-Lopes
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
| | - Roberta Marongiu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
- Neurological Surgery Department, Weill Cornell Medicine, New York, New York 10065, USA
| | - Michael J Glass
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
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21
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Winek K, Tzur Y, Soreq H. Biological underpinnings of sex differences in neurological disorders. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2022; 164:27-67. [PMID: 36038206 DOI: 10.1016/bs.irn.2022.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The importance of sex differences in neurological disorders has been increasingly acknowledged in recent clinical and basic research studies, but the complex biology and genetics underlying sex-linked biological heterogeneity and its brain-to-body impact remained incompletely understood. Men and women differ substantially in their susceptibility to certain neurological diseases, in the severity of symptoms, prognosis as well as the nature and efficacy of their response to treatments. The detailed mechanisms underlying these differences, especially at the molecular level, are being addressed in many studies but leave a lot to be further revealed. Here, we provide an overview of recent advances in our understanding of how sex differences in the brain and brain-body signaling contribute to neurological disorders and further present some future prospects entailed in terms of diagnostics and therapeutics.
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Affiliation(s)
- Katarzyna Winek
- The Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel; The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yonat Tzur
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hermona Soreq
- The Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel; The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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22
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Midhun T, Krishna SS, Wilson SK. Tetrahydrobiopterin and Its Multiple Roles in Neuropsychological Disorders. Neurochem Res 2022; 47:1202-1211. [PMID: 35142994 DOI: 10.1007/s11064-022-03543-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
Abstract
Tetrahydrobiopterin (BH4) is a multifunctional co-factor of various enzymes and a substantial amount of studies have shown BH4 as a key regulator in the synthesis of neurotransmitters such as serotonin, nor-epinephrine as well as dopamine. The imbalance of BH4 may affect neurotransmitter production which can lead to many abnormalities in CNS. This article reviews the role of BH4 in neurodegenerative and neurodevelopmental disorders. We focus on the therapeutic potential of BH4 in various brain diseases that involves neurotransmitters and attempt to address how the modulation of BH4 may provide a novel strategy in various neuropsychological conditions.
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Affiliation(s)
- Midhun T
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi, 682041, Kerala, India
| | - S Swathi Krishna
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi, 682041, Kerala, India
| | - Samson K Wilson
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi, 682041, Kerala, India.
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23
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Serebrovska ZO, Xi L, Tumanovska LV, Shysh AM, Goncharov SV, Khetsuriani M, Kozak TO, Pashevin DA, Dosenko VE, Virko SV, Kholin VA, Grib ON, Utko NA, Egorov E, Polischuk AO, Serebrovska TV. Response of Circulating Inflammatory Markers to Intermittent Hypoxia-Hyperoxia Training in Healthy Elderly People and Patients with Mild Cognitive Impairment. Life (Basel) 2022; 12:life12030432. [PMID: 35330183 PMCID: PMC8953753 DOI: 10.3390/life12030432] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 12/28/2022] Open
Abstract
Intermittent hypoxia-hyperoxia training (IHHT) is a non-pharmacological therapeutic modality for management of some chronic- and age-related pathologies, such as Alzheimer’s disease (AD). Our previous studies demonstrated significant improvement of cognitive function after IHHT in the patients with mild cognitive impairment (MCI). The present study further investigated the effects of IHHT on pro-inflammatory factors in healthy elderly individuals and patients with early signs of AD. Twenty-nine subjects (13 healthy subjects without signs of cognitive impairment syndrome and 16 patients diagnosed with MCI; age 52 to 76 years) were divided into four groups: Healthy+Sham (n = 7), Healthy+IHHT (n = 6), MCI+Sham (n = 6), and MCI+IHHT (n = 10). IHHT was carried out 5 days per week for 3 weeks (total 15 sessions), and each daily session included 4 cycles of 5-min hypoxia (12% FIO2) and 3-min hyperoxia (33% FIO2). Decline in cognitive function indices was observed initially in both MCI+Sham and MCI+IHHT groups. The sham training did not alter any of the parameters, whereas IHHT resulted in improvement in latency of cognitive evoked potentials, along with elevation in APP110, GDF15 expression, and MMP9 activity in both healthy subjects and those with MCI. Increased MMP2 activity, HMGB1, and P-selectin expression and decreased NETs formation and Aβ expression were also observed in the MCI+IHHT group. There was a negative correlation between MoCA score and the plasma GDF15 expression (R = −0.5799, p < 0.05) before the initiation of IHHT. The enhanced expression of GDF15 was also associated with longer latency of the event-related potentials P330 and N200 (R = 0.6263, p < 0.05 and R = 0.5715, p < 0.05, respectively). In conclusion, IHHT upregulated circulating levels of some inflammatory markers, which may represent potential triggers for cellular adaptive reprogramming, leading to therapeutic effects against cognitive dysfunction and neuropathological changes during progression of AD. Further investigation is needed to clarify if there is a causative relationship between the improved cognitive function and the elevated inflammatory markers following IHHT.
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Affiliation(s)
- Zoya O. Serebrovska
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, 01024 Kyiv, Ukraine; (L.V.T.); (A.M.S.); (S.V.G.); (M.K.); (T.O.K.); (D.A.P.); (V.E.D.); (A.O.P.); (T.V.S.)
- Correspondence: (Z.O.S.); (L.X.)
| | - Lei Xi
- Pauley Heart Center, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298-0204, USA
- Correspondence: (Z.O.S.); (L.X.)
| | - Lesya V. Tumanovska
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, 01024 Kyiv, Ukraine; (L.V.T.); (A.M.S.); (S.V.G.); (M.K.); (T.O.K.); (D.A.P.); (V.E.D.); (A.O.P.); (T.V.S.)
| | - Angela M. Shysh
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, 01024 Kyiv, Ukraine; (L.V.T.); (A.M.S.); (S.V.G.); (M.K.); (T.O.K.); (D.A.P.); (V.E.D.); (A.O.P.); (T.V.S.)
| | - Sergii V. Goncharov
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, 01024 Kyiv, Ukraine; (L.V.T.); (A.M.S.); (S.V.G.); (M.K.); (T.O.K.); (D.A.P.); (V.E.D.); (A.O.P.); (T.V.S.)
| | - Michael Khetsuriani
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, 01024 Kyiv, Ukraine; (L.V.T.); (A.M.S.); (S.V.G.); (M.K.); (T.O.K.); (D.A.P.); (V.E.D.); (A.O.P.); (T.V.S.)
| | - Taisia O. Kozak
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, 01024 Kyiv, Ukraine; (L.V.T.); (A.M.S.); (S.V.G.); (M.K.); (T.O.K.); (D.A.P.); (V.E.D.); (A.O.P.); (T.V.S.)
| | - Denis A. Pashevin
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, 01024 Kyiv, Ukraine; (L.V.T.); (A.M.S.); (S.V.G.); (M.K.); (T.O.K.); (D.A.P.); (V.E.D.); (A.O.P.); (T.V.S.)
| | - Victor E. Dosenko
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, 01024 Kyiv, Ukraine; (L.V.T.); (A.M.S.); (S.V.G.); (M.K.); (T.O.K.); (D.A.P.); (V.E.D.); (A.O.P.); (T.V.S.)
| | - Sergii V. Virko
- Lashkariov Institute of Semiconductor Physics, National Academy of Sciences, 41 Nauki Ave., 03028 Kyiv, Ukraine;
| | - Viktor A. Kholin
- Department of Age Physiology and Pathology of Nervous System, Chebotarev Institute of Gerontology NAMS of Ukraine, 04114 Kyiv, Ukraine; (V.A.K.); (O.N.G.); (N.A.U.)
| | - Oksana N. Grib
- Department of Age Physiology and Pathology of Nervous System, Chebotarev Institute of Gerontology NAMS of Ukraine, 04114 Kyiv, Ukraine; (V.A.K.); (O.N.G.); (N.A.U.)
| | - Natalie A. Utko
- Department of Age Physiology and Pathology of Nervous System, Chebotarev Institute of Gerontology NAMS of Ukraine, 04114 Kyiv, Ukraine; (V.A.K.); (O.N.G.); (N.A.U.)
| | - Egor Egorov
- CELLGYM Technologies GmbH, 14193 Berlin, Germany;
| | - Anna O. Polischuk
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, 01024 Kyiv, Ukraine; (L.V.T.); (A.M.S.); (S.V.G.); (M.K.); (T.O.K.); (D.A.P.); (V.E.D.); (A.O.P.); (T.V.S.)
| | - Tetiana V. Serebrovska
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, 01024 Kyiv, Ukraine; (L.V.T.); (A.M.S.); (S.V.G.); (M.K.); (T.O.K.); (D.A.P.); (V.E.D.); (A.O.P.); (T.V.S.)
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24
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Tang AS, Oskotsky T, Havaldar S, Mantyh WG, Bicak M, Solsberg CW, Woldemariam S, Zeng B, Hu Z, Oskotsky B, Dubal D, Allen IE, Glicksberg BS, Sirota M. Deep phenotyping of Alzheimer's disease leveraging electronic medical records identifies sex-specific clinical associations. Nat Commun 2022; 13:675. [PMID: 35115528 PMCID: PMC8814236 DOI: 10.1038/s41467-022-28273-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 01/18/2022] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's Disease (AD) is a neurodegenerative disorder that is still not fully understood. Sex modifies AD vulnerability, but the reasons for this are largely unknown. We utilize two independent electronic medical record (EMR) systems across 44,288 patients to perform deep clinical phenotyping and network analysis to gain insight into clinical characteristics and sex-specific clinical associations in AD. Embeddings and network representation of patient diagnoses demonstrate greater comorbidity interactions in AD in comparison to matched controls. Enrichment analysis identifies multiple known and new diagnostic, medication, and lab result associations across the whole cohort and in a sex-stratified analysis. With this data-driven method of phenotyping, we can represent AD complexity and generate hypotheses of clinical factors that can be followed-up for further diagnostic and predictive analyses, mechanistic understanding, or drug repurposing and therapeutic approaches.
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Affiliation(s)
- Alice S Tang
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA.
- Graduate Program in Bioengineering, UCSF, San Francisco, CA, USA.
- School of Medicine, UCSF, San Francisco, CA, USA.
| | - Tomiko Oskotsky
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
- Department of Pediatrics, UCSF, San Francisco, CA, USA
| | - Shreyas Havaldar
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - William G Mantyh
- Department of Neurology, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Mesude Bicak
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Caroline Warly Solsberg
- Pharmaceutical Sciences and Pharmacogenomics, UCSF, San Francisco, CA, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Memory and Aging Center, UCSF, San Francisco, CA, USA
| | - Sarah Woldemariam
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | - Billy Zeng
- School of Medicine, UCSF, San Francisco, CA, USA
| | - Zicheng Hu
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | - Boris Oskotsky
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | - Dena Dubal
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Isabel E Allen
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, USA
| | - Benjamin S Glicksberg
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA.
- Department of Pediatrics, UCSF, San Francisco, CA, USA.
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