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Saliu IO, Zhao G. New insights into astrocyte diversity from the lens of transcriptional regulation and their implications for neurodegenerative disease treatments. Neural Regen Res 2024; 19:2335-2336. [PMID: 38526262 PMCID: PMC11090421 DOI: 10.4103/nrr.nrr-d-23-01790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/13/2023] [Accepted: 12/30/2023] [Indexed: 03/26/2024] Open
Affiliation(s)
| | - Guoyan Zhao
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
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2
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Tong MK, Thakur A, Yang T, Wong SK, Li WK, Lee Y. Amyloid-β oligomer-induced neurotoxicity by exosomal interactions between neuron and microglia. Biochem Biophys Res Commun 2024; 727:150312. [PMID: 38924962 DOI: 10.1016/j.bbrc.2024.150312] [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: 06/07/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
A hallmark of Alzheimer's disease (AD) is amyloid-β (Aβ) plaque deposition in the brain, causing deficits in cognitive function. Amyloid-beta oligomers (AβOs), the soluble precursor peptides producing Aβ plaques, also produce neurotoxicity and microgliosis together with glycolytic reprogramming. Recently, monocarboxylate transporter 1 (MCT1), a key glycolysis regulator, and its ancillary protein, CD147, are found to play an important role in the secretion of exosomes, 30-200 nm vesicles in size, which are considered as toxic molecule carriers in AD. However, the effect of low-concentration AβOs (1 nM) on microglia MCT1 and CD147 expression as well as 1 nM AβOs-treated microglia-derived exosomes on neuronal toxicity remain largely elusive. In this study, 1 nM AβOs induce significant axonopathy and microgliosis. Furthermore, 1 nM AβOs-treated neurons- or microglia-derived exosomes produce axonopathy through their autologous or heterologous uptake by neurons, supporting the role of exosomes as neurotoxicity mediators in AD. Interestingly, MCT1 and CD147 are enhanced in microglia by treatment with 1 nM AβOs or exosomes from 1 nM AβOs-treated- microglia or neurons, suggesting the implication of AβOs-induced enhanced MCT1 and CD147 in microglia with AD neuropathogenesis, which is consistent with the in-silico analysis of the single cell RNA sequencing data from microglia in mouse models of AD and AD patients.
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Affiliation(s)
- Man Kit Tong
- Department of Neurosciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Abhimanyu Thakur
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Tian Yang
- Department of Neurosciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Sze Kai Wong
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Wing Kar Li
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Youngjin Lee
- Department of Neurosciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
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3
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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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4
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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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5
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Duggan MR, Gomez GT, Joynes CM, Bilgel M, Chen J, Fattorelli N, Hohman TJ, Mancuso R, Cordon J, Castellano T, Koran MEI, Candia J, Lewis A, Moghekar A, Ashton NJ, Kac PR, Karikari TK, Blennow K, Zetterberg H, Martinez-Muriana A, De Strooper B, Thambisetty M, Ferrucci L, Gottesman RF, Coresh J, Resnick SM, Walker KA. Proteome-wide analysis identifies plasma immune regulators of amyloid-beta progression. Brain Behav Immun 2024; 120:604-619. [PMID: 38977137 DOI: 10.1016/j.bbi.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/07/2024] [Accepted: 07/04/2024] [Indexed: 07/10/2024] Open
Abstract
While immune function is known to play a mechanistic role in Alzheimer's disease (AD), whether immune proteins in peripheral circulation influence the rate of amyloid-β (Aβ) progression - a central feature of AD - remains unknown. In the Baltimore Longitudinal Study of Aging, we quantified 942 immunological proteins in plasma and identified 32 (including CAT [catalase], CD36 [CD36 antigen], and KRT19 [keratin 19]) associated with rates of cortical Aβ accumulation measured with positron emission tomography (PET). Longitudinal changes in a subset of candidate proteins also predicted Aβ progression, and the mid- to late-life (20-year) trajectory of one protein, CAT, was associated with late-life Aβ-positive status in the Atherosclerosis Risk in Communities (ARIC) study. Genetic variation that influenced plasma levels of CAT, CD36 and KRT19 predicted rates of Aβ accumulation, including causal relationships with Aβ PET levels identified with two-sample Mendelian randomization. In addition to associations with tau PET and plasma AD biomarker changes, as well as expression patterns in human microglia subtypes and neurovascular cells in AD brain tissue, we showed that 31 % of candidate proteins were related to mid-life (20-year) or late-life (8-year) dementia risk in ARIC. Our findings reveal plasma proteins associated with longitudinal Aβ accumulation, and identify specific peripheral immune mediators that may contribute to the progression of AD pathophysiology.
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Affiliation(s)
- Michael R Duggan
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Gabriela T Gomez
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cassandra M Joynes
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Murat Bilgel
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Jingsha Chen
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Nicola Fattorelli
- VIB Center for Brain and Disease Research, Flanders Institute for Biotechnology, Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Renzo Mancuso
- Microglia and Inflammation in Neurological Disorders Laboratory, Center for Molecular Neurology, Flanders Institute for Biotechnology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jenifer Cordon
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Tonnar Castellano
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mary Ellen I Koran
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julián Candia
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Alexandria Lewis
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas J Ashton
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden; Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK; NIHR Biomedical Research Center for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation, London, UK; Center for Age-Related Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Przemysław R Kac
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden
| | - Thomas K Karikari
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden; Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; ICM Institute, Pitié-Salpêtrière University Hospital, Sorbonne University, Paris, France; First Affiliated Hospital, University of Science and Technology of China, Anhui, PR China
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; Department of Neurodegenerative Disease, University College London Institute of Neurology, London, UK; UK Dementia Research Institute, University College London, London, UK; Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong Special Administrative Region; Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Anna Martinez-Muriana
- VIB Center for Brain and Disease Research, Flanders Institute for Biotechnology, Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Bart De Strooper
- VIB Center for Brain and Disease Research, Flanders Institute for Biotechnology, Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; UK Dementia Research Institute, University College London, London, UK
| | - Madhav Thambisetty
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Rebecca F Gottesman
- Stroke Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Josef Coresh
- Departments of Population Health and Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Keenan A Walker
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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Soraci L, Corsonello A, Paparazzo E, Montesanto A, Piacenza F, Olivieri F, Gambuzza ME, Savedra EV, Marino S, Lattanzio F, Biscetti L. Neuroinflammaging: A Tight Line Between Normal Aging and Age-Related Neurodegenerative Disorders. Aging Dis 2024; 15:1726-1747. [PMID: 38300639 PMCID: PMC11272206 DOI: 10.14336/ad.2023.1001] [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: 08/12/2023] [Accepted: 10/01/2023] [Indexed: 02/02/2024] Open
Abstract
Aging in the healthy brain is characterized by a low-grade, chronic, and sterile inflammatory process known as neuroinflammaging. This condition, mainly consisting in an up-regulation of the inflammatory response at the brain level, contributes to the pathogenesis of age-related neurodegenerative disorders. Development of this proinflammatory state involves the interaction between genetic and environmental factors, able to induce age-related epigenetic modifications. Indeed, the exposure to environmental compounds, drugs, and infections, can contribute to epigenetic modifications of DNA methylome, histone fold proteins, and nucleosome positioning, leading to epigenetic modulation of neuroinflammatory responses. Furthermore, some epigenetic modifiers, which combine and interact during the life course, can contribute to modeling of epigenome dynamics to sustain, or dampen the neuroinflammatory phenotype. The aim of this review is to summarize current knowledge about neuroinflammaging with a particular focus on epigenetic mechanisms underlying the onset and progression of neuroinflammatory cascades in the central nervous system; furthermore, we describe some diagnostic biomarkers that may contribute to increase diagnostic accuracy and help tailor therapeutic strategies in patients with neurodegenerative diseases.
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Affiliation(s)
- Luca Soraci
- Unit of Geriatric Medicine, Italian National Research Center of Aging (IRCCS INRCA), Cosenza, Italy
| | - Andrea Corsonello
- Unit of Geriatric Medicine, Italian National Research Center of Aging (IRCCS INRCA), Cosenza, Italy
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Ersilia Paparazzo
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, Italian National Research Center of Aging (IRCCS INRCA), IRCCS INRCA, Ancona, Italy
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
- Clinic of Laboratory and Precision Medicine, Italian National Research Center of Aging (IRCCS INRCA), Ancona, Italy
| | | | | | - Silvia Marino
- IRCCS Centro Neurolesi "Bonino-Pulejo", Messina, Italy
| | | | - Leonardo Biscetti
- Section of Neurology, Italian National Research Center on Aging (IRCCS INRCA), Ancona, Italy
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7
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Methi A, Islam MR, Kaurani L, Sakib MS, Krüger DM, Pena T, Burkhardt S, Liebetanz D, Fischer A. A Single-Cell Transcriptomic Analysis of the Mouse Hippocampus After Voluntary Exercise. Mol Neurobiol 2024; 61:5628-5645. [PMID: 38217668 PMCID: PMC11249425 DOI: 10.1007/s12035-023-03869-9] [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: 07/26/2023] [Accepted: 11/29/2023] [Indexed: 01/15/2024]
Abstract
Exercise has been recognized as a beneficial factor for cognitive health, particularly in relation to the hippocampus, a vital brain region responsible for learning and memory. Previous research has demonstrated that exercise-mediated improvement of learning and memory in humans and rodents correlates with increased adult neurogenesis and processes related to enhanced synaptic plasticity. Nevertheless, the underlying molecular mechanisms are not fully understood. With the aim to further elucidate these mechanisms, we provide a comprehensive dataset of the mouse hippocampal transcriptome at the single-cell level after 4 weeks of voluntary wheel-running. Our analysis provides a number of interesting observations. For example, the results suggest that exercise affects adult neurogenesis by accelerating the maturation of a subpopulation of Prdm16-expressing neurons. Moreover, we uncover the existence of an intricate crosstalk among multiple vital signaling pathways such as NF-κB, Wnt/β-catenin, Notch, and retinoic acid (RA) pathways altered upon exercise in a specific cluster of excitatory neurons within the Cornu Ammonis (CA) region of the hippocampus. In conclusion, our study provides an important resource dataset and sheds further light on the molecular changes induced by exercise in the hippocampus. These findings have implications for developing targeted interventions aimed at optimizing cognitive health and preventing age-related cognitive decline.
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Affiliation(s)
- Aditi Methi
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Md Rezaul Islam
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Lalit Kaurani
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - M Sadman Sakib
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Dennis M Krüger
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
- Bioinformatics Unit, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Tonatiuh Pena
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
- Bioinformatics Unit, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Susanne Burkhardt
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - David Liebetanz
- Department of Neurology, University Medical Center, Göttingen, Germany
| | - André Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany.
- Department for Psychiatry and Psychotherapy, University Medical Center of Göttingen, Georg-August University, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
- DZHK (German Center for Cardiovascular Research), Partner Site, Göttingen, Germany.
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8
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Bedwell L, Mavrotas M, Demchenko N, Yaa RM, Willis B, Demianova Z, Syed N, Whitwell HJ, Nott A. FANS Unfixed: Isolation and Proteomic Analysis of Mouse Cell Type-Specific Brain Nuclei. J Proteome Res 2024. [PMID: 39056441 DOI: 10.1021/acs.jproteome.4c00161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Epigenetic-mediated gene regulation orchestrates brain cell-type gene expression programs, and epigenetic dysregulation is a major driver of aging and disease-associated changes. Proteins that mediate gene regulation are mostly localized to the nucleus; however, nuclear-localized proteins are often underrepresented in gene expression studies and have been understudied in the context of the brain. To address this challenge, we have optimized an approach for nuclei isolation that is compatible with proteomic analysis. This was coupled to a mass spectrometry protocol for detecting proteins in low-concentration samples. We have generated nuclear proteomes for neurons, microglia, and oligodendrocytes from the mouse brain cortex and identified cell-type nuclear proteins associated with chromatin structure and organization, chromatin modifiers such as transcription factors, and RNA-binding proteins, among others. Our nuclear proteomics platform paves the way for assessing brain cell type changes in the nuclear proteome across health and disease, such as neurodevelopmental, aging, neurodegenerative, and neuroinflammatory conditions. Data are available via ProteomeXchange with the identifier PXD053515.
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Affiliation(s)
- Lucy Bedwell
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
- UK Dementia Research Institute, Imperial College London, London W12 0NN, U.K
| | - Myrto Mavrotas
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
| | - Nikita Demchenko
- MRC Laboratory of Medical Sciences, Du Cane Road, London W12 0NN, U.K
| | - Reuben M Yaa
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
- UK Dementia Research Institute, Imperial College London, London W12 0NN, U.K
| | - Brittannie Willis
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London W12 0NN, U.K
| | | | - Nelofer Syed
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
| | - Harry J Whitwell
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London W12 0NN, U.K
| | - Alexi Nott
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
- UK Dementia Research Institute, Imperial College London, London W12 0NN, U.K
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9
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Ren A, Chen F, Ren C, Yang M, Wang C, Feng X, Zhang F. Rapid Screening of Biomarkers in KYSE-150 Cells Exposed to Polycyclic Aromatic Hydrocarbons via Inkjet Printing Single-Cell Mass Spectrometry. Anal Chem 2024. [PMID: 39052489 DOI: 10.1021/acs.analchem.4c02332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Single-cell analysis by mass spectrometry (MS) is emerging as a powerful tool that not only contributes to cellular heterogeneity but also offers an unprecedented opportunity to predict pathology onset and facilitates novel biomarker discovery. However, the development of single-cell MS analysis techniques with a focus on sample extraction, separation, and ionization methods for volume-limited samples and complexity of cellular samples are still a big challenge. In this study, we present a high-throughput approach to inkjet drop on demand printing single-cell MS for rapid screening of biomarkers of polycyclic aromatic hydrocarbon (PAH) exposure at the KYSE-150 cell, aiming to elucidate the pathogenesis of PAH-induced esophageal cancer. With an analytical bulk KYSE-150 cell throughput of up to 51 cells per minute, the method provides a new opportunity for simultaneous single-cell analysis of multiple biomarkers. We screened 930 characteristic ions from 3,683 detected peak signals and identified 91 distinctive molecules that exhibited significant differences under various concentrations of PAH exposure. These molecules have potential as clinical diagnostic biomarkers. Additionally, the current study identifies specific biomarkers that behave completely opposite in single-cell and multicell lipidomics as the concentration of PAH changes. These biomarkers potentially subdivide KYSE-150 cells into PAH-sensitive and PAH-insensitive types, providing a basis for revealing PAH toxicity and disease pathogenesis from the heterogeneity of cellular metabolism.
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Affiliation(s)
- Ai Ren
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Fengming Chen
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Chenjie Ren
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Minli Yang
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Chang Wang
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Xuesong Feng
- School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Feng Zhang
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
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10
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Mathys H, Boix CA, Akay LA, Xia Z, Davila-Velderrain J, Ng AP, Jiang X, Abdelhady G, Galani K, Mantero J, Band N, James BT, Babu S, Galiana-Melendez F, Louderback K, Prokopenko D, Tanzi RE, Bennett DA, Tsai LH, Kellis M. Single-cell multiregion dissection of Alzheimer's disease. Nature 2024:10.1038/s41586-024-07606-7. [PMID: 39048816 DOI: 10.1038/s41586-024-07606-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 05/24/2024] [Indexed: 07/27/2024]
Abstract
Alzheimer's disease is the leading cause of dementia worldwide, but the cellular pathways that underlie its pathological progression across brain regions remain poorly understood1-3. Here we report a single-cell transcriptomic atlas of six different brain regions in the aged human brain, covering 1.3 million cells from 283 post-mortem human brain samples across 48 individuals with and without Alzheimer's disease. We identify 76 cell types, including region-specific subtypes of astrocytes and excitatory neurons and an inhibitory interneuron population unique to the thalamus and distinct from canonical inhibitory subclasses. We identify vulnerable populations of excitatory and inhibitory neurons that are depleted in specific brain regions in Alzheimer's disease, and provide evidence that the Reelin signalling pathway is involved in modulating the vulnerability of these neurons. We develop a scalable method for discovering gene modules, which we use to identify cell-type-specific and region-specific modules that are altered in Alzheimer's disease and to annotate transcriptomic differences associated with diverse pathological variables. We identify an astrocyte program that is associated with cognitive resilience to Alzheimer's disease pathology, tying choline metabolism and polyamine biosynthesis in astrocytes to preserved cognitive function late in life. Together, our study develops a regional atlas of the ageing human brain and provides insights into cellular vulnerability, response and resilience to Alzheimer's disease pathology.
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Affiliation(s)
- Hansruedi Mathys
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Carles A Boix
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computational and Systems Biology Program, MIT, Cambridge, MA, USA
| | - Leyla Anne Akay
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Ziting Xia
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology Program, MIT, Cambridge, MA, USA
| | | | - Ayesha P Ng
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Xueqiao Jiang
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Ghada Abdelhady
- University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kyriaki Galani
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julio Mantero
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neil Band
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Benjamin T James
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sudhagar Babu
- University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Fabiola Galiana-Melendez
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Kate Louderback
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Dmitry Prokopenko
- Genetics and Aging Research Unit, McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Li-Huei Tsai
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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11
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Ma Z, Zhang W, Wang C, Su Y, Yi C, Niu J. A New Acquaintance of Oligodendrocyte Precursor Cells in the Central Nervous System. Neurosci Bull 2024:10.1007/s12264-024-01261-8. [PMID: 39042298 DOI: 10.1007/s12264-024-01261-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/21/2024] [Indexed: 07/24/2024] Open
Abstract
Oligodendrocyte precursor cells (OPCs) are a heterogeneous multipotent population in the central nervous system (CNS) that appear during embryogenesis and persist as resident cells in the adult brain parenchyma. OPCs could generate oligodendrocytes to participate in myelination. Recent advances have renewed our knowledge of OPC biology by discovering novel markers of oligodendroglial cells, the myelin-independent roles of OPCs, and the regulatory mechanism of OPC development. In this review, we will explore the updated knowledge on OPC identity, their multifaceted roles in the CNS in health and diseases, as well as the regulatory mechanisms that are involved in their developmental stages, which hopefully would contribute to a further understanding of OPCs and attract attention in the field of OPC biology.
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Affiliation(s)
- Zexuan Ma
- Department of Histology and Embryology, College of basic medicine, Third Military Medical University, Chongqing, 400038, China
| | - Wei Zhang
- Department of Histology and Embryology, College of basic medicine, Third Military Medical University, Chongqing, 400038, China
| | - Chenmeng Wang
- Department of Histology and Embryology, College of basic medicine, Third Military Medical University, Chongqing, 400038, China
- Research Centre, Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Yixun Su
- Research Centre, Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Chenju Yi
- Research Centre, Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, China.
- Shenzhen Key Laboratory of Chinese Medicine Active substance screening and Translational Research, Shenzhen, 518107, China.
| | - Jianqin Niu
- Department of Histology and Embryology, College of basic medicine, Third Military Medical University, Chongqing, 400038, China.
- Chongqing Key Laboratory of Neurobiology, Chongqing, 400038, China.
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12
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Yslas AR, Park R, Nishimura N, Lee E. Monomeric and oligomeric amyloid-β cause distinct Alzheimer's disease pathophysiological characteristics in astrocytes in human glymphatics-on-chip models. LAB ON A CHIP 2024. [PMID: 39037244 DOI: 10.1039/d4lc00287c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Alzheimer's disease (AD) is marked by the aggregation of extracellular amyloid-β (Aβ) and astrocyte dysfunction. For Aβ oligomers or aggregates to be formed, there must be Aβ monomers present; however, the roles of monomeric Aβ (mAβ) and oligomeric Aβ (oAβ) in astrocyte pathogenesis are poorly understood. We cultured astrocytes in a brain-mimicking three-dimensional (3D) extracellular matrix and revealed that both mAβ and oAβ caused astrocytic atrophy and hyper-reactivity, but showed distinct Ca2+ changes in astrocytes. This 3D culture evolved into a microfluidic glymphatics-on-chip model containing astrocytes and endothelial cells with the interstitial fluid (ISF). The glymphatics-on-chip model not only reproduced the astrocytic atrophy, hyper-reactivity, and Ca2+ changes induced by mAβ and oAβ, but recapitulated that the components of the dystrophin-associated complex (DAC) and aquaporin-4 (AQP4) were properly maintained by the ISF, and dysregulated by mAβ and oAβ. Collectively, mAβ and oAβ cause distinct AD pathophysiological characteristics in the astrocytes.
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Affiliation(s)
- Aria R Yslas
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA.
| | - Rena Park
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA.
| | - Nozomi Nishimura
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA.
| | - Esak Lee
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA.
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13
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Wang J, Fonseca GJ, Ding J. scSemiProfiler: Advancing large-scale single-cell studies through semi-profiling with deep generative models and active learning. Nat Commun 2024; 15:5989. [PMID: 39013867 PMCID: PMC11252419 DOI: 10.1038/s41467-024-50150-1] [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: 11/29/2023] [Accepted: 06/28/2024] [Indexed: 07/18/2024] Open
Abstract
Single-cell sequencing is a crucial tool for dissecting the cellular intricacies of complex diseases. Its prohibitive cost, however, hampers its application in expansive biomedical studies. Traditional cellular deconvolution approaches can infer cell type proportions from more affordable bulk sequencing data, yet they fall short in providing the detailed resolution required for single-cell-level analyses. To overcome this challenge, we introduce "scSemiProfiler", an innovative computational framework that marries deep generative models with active learning strategies. This method adeptly infers single-cell profiles across large cohorts by fusing bulk sequencing data with targeted single-cell sequencing from a few rigorously chosen representatives. Extensive validation across heterogeneous datasets verifies the precision of our semi-profiling approach, aligning closely with true single-cell profiling data and empowering refined cellular analyses. Originally developed for extensive disease cohorts, "scSemiProfiler" is adaptable for broad applications. It provides a scalable, cost-effective solution for single-cell profiling, facilitating in-depth cellular investigation in various biological domains.
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Affiliation(s)
- Jingtao Wang
- Meakins-Christe Laboratories, Research Institute of McGill University Health Centre, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada
| | - Gregory J Fonseca
- Meakins-Christe Laboratories, Research Institute of McGill University Health Centre, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada
- Quantitative Life Sciences, McGill University, 845 Rue Sherbrooke Ouest, Montreal, H3A 0G4, Quebec, Canada
| | - Jun Ding
- Meakins-Christe Laboratories, Research Institute of McGill University Health Centre, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Decarie Blvd, Montreal, H4A 3J1, Quebec, Canada.
- Quantitative Life Sciences, McGill University, 845 Rue Sherbrooke Ouest, Montreal, H3A 0G4, Quebec, Canada.
- School of Computer Science, McGill University, 3480 Rue University, Montreal, H3A 2A7, Quebec, Canada.
- Mila-Quebec AI Institute, 6666 Rue Saint-Urbain, Montreal, H2S 3H1, Quebec, Canada.
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14
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Ganesh A, Choudhury W, Coutellier L. Early spatial recognition memory deficits in 5XFAD female mice are associated with disruption of prefrontal parvalbumin neurons. Brain Res 2024; 1841:149122. [PMID: 39009061 DOI: 10.1016/j.brainres.2024.149122] [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: 06/06/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/17/2024]
Abstract
Women have a two-fold increased risk of developing Alzheimer's disease (AD) than men, yet the underlying mechanisms of this sex-specific vulnerability remain unknown. Here, we aimed at determining in the 5XFAD mouse model whether deficits in prefrontal-dependent cognitive functions, which are impacted in the preclinical stages of AD, appear earlier in females, and whether these cognitive deficits are associated with alterations in the activity of prefrontal parvalbumin (PV)-neurons that regulate prefrontal circuits activity. We observed that 3.5-month-old 5XFAD females, but not males, display impairments in spatial short-term recognition memory, a function that relies on the integrity of the prefrontal cortex. Hippocampal-dependent cognitive functions were intact in both sexes. We then observed that 5XFAD females have more prefrontal PV neurons expressing the marker of chronic activity FosB; this was inversely correlated with prefrontal-dependent cognitive performances. Our findings show for the first time sex-specific, early deregulation of prefrontal PV neurons activity, which is associated with early appearance of prefrontal-dependent cognitive functions in 5XFAD females providing a potential novel mechanism to the increased risk to AD in females.
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Affiliation(s)
- Anish Ganesh
- Department of Psychology, The Ohio State University, Columbus, OH, USA
| | - Wajih Choudhury
- Department of Psychology, The Ohio State University, Columbus, OH, USA
| | - Laurence Coutellier
- Department of Psychology, The Ohio State University, Columbus, OH, USA; Department of Neuroscience, The Ohio State University, Columbus, OH, USA.
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15
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Craig GA, Ryan L, Thapar J, McNamara NB, Hoffmann A, Page D, Rose J, Cox SR, Miron VE. Reflective imaging of myelin integrity in the human and mouse central nervous systems. Front Cell Neurosci 2024; 18:1408182. [PMID: 39049821 PMCID: PMC11266064 DOI: 10.3389/fncel.2024.1408182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/13/2024] [Indexed: 07/27/2024] Open
Abstract
The structural integrity of myelin sheaths in the central nervous system (CNS) is crucial for the maintenance of its function. Electron microscopy (EM) is the gold standard for visualizing individual myelin sheaths. However, the tissue processing involved can induce artifacts such as shearing of myelin, which can be difficult to distinguish from true myelin abnormalities. Spectral confocal reflectance (SCoRe) microscopy is an imaging technique that leverages the differential refractive indices of compacted CNS myelin in comparison to surrounding parenchyma to detect individual compact myelin internodes with reflected light, positioning SCoRe as a possible complementary method to EM to assess myelin integrity. Whether SCoRe is sensitive enough to detect losses in myelin compaction when myelin quantity is otherwise unaffected has not yet been directly tested. Here, we assess the capacity of SCoRe to detect differences in myelin compaction in two mouse models that exhibit a loss of myelin compaction without demyelination: microglia-deficient mice (Csf1r-FIRE Δ/Δ) and wild-type mice fed with the CSF1R inhibitor PLX5622. In addition, we compare the ability to detect compact myelin sheaths using SCoRe in fixed-frozen versus paraffin-embedded mouse tissue. Finally, we show that SCoRe can successfully detect individual sheaths in aged human paraffin-embedded samples of deep white matter regions. As such, we find SCoRe to be an attractive technique to investigate myelin integrity, with sufficient sensitivity to detect myelin ultrastructural abnormalities and the ability to perform equally well in tissue preserved using different methods.
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Affiliation(s)
- Georgina A. Craig
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- United Kingdom Dementia Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Lucy Ryan
- United Kingdom Dementia Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jessica Thapar
- Department of Immunology, The University of Toronto, Toronto, ON, Canada
| | - Niamh B. McNamara
- United Kingdom Dementia Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Alana Hoffmann
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- United Kingdom Dementia Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Danielle Page
- Lothian Birth Cohorts, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jamie Rose
- United Kingdom Dementia Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Simon R. Cox
- Lothian Birth Cohorts, The University of Edinburgh, Edinburgh, United Kingdom
| | - Veronique E. Miron
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
- United Kingdom Dementia Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
- Department of Immunology, The University of Toronto, Toronto, ON, Canada
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16
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Wang Q, Antone J, Alsop E, Reiman R, Funk C, Bendl J, Dudley JT, Liang WS, Karr TL, Roussos P, Bennett DA, De Jager PL, Serrano GE, Beach TG, Van Keuren-Jensen K, Mastroeni D, Reiman EM, Readhead BP. Single cell transcriptomes and multiscale networks from persons with and without Alzheimer's disease. Nat Commun 2024; 15:5815. [PMID: 38987616 PMCID: PMC11237088 DOI: 10.1038/s41467-024-49790-0] [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: 10/27/2023] [Accepted: 06/13/2024] [Indexed: 07/12/2024] Open
Abstract
The emergence of single nucleus RNA sequencing (snRNA-seq) offers to revolutionize the study of Alzheimer's disease (AD). Integration with complementary multiomics data such as genetics, proteomics and clinical data provides powerful opportunities to link cell subpopulations and molecular networks with a broader disease-relevant context. We report snRNA-seq profiles from superior frontal gyrus samples from 101 well characterized subjects from the Banner Brain and Body Donation Program in combination with whole genome sequences. We report findings that link common AD risk variants with CR1 expression in oligodendrocytes as well as alterations in hematological parameters. We observed an AD-associated CD83(+) microglial subtype with unique molecular networks and which is associated with immunoglobulin IgG4 production in the transverse colon. Our major observations were replicated in two additional, independent snRNA-seq data sets. These findings illustrate the power of multi-tissue molecular profiling to contextualize snRNA-seq brain transcriptomics and reveal disease biology.
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Affiliation(s)
- Qi Wang
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Jerry Antone
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Eric Alsop
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Rebecca Reiman
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Cory Funk
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jaroslav Bendl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joel T Dudley
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Winnie S Liang
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Timothy L Karr
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Philip L De Jager
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | | | - Diego Mastroeni
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Eric M Reiman
- Banner Alzheimer's Institute, Phoenix, AZ, 85006, USA
| | - Benjamin P Readhead
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA.
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17
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Ravichandar R, Gadelkarim F, Muthaiah R, Glynos N, Murlanova K, Rai NK, Saraswat D, Polanco JJ, Dutta R, Pal D, Sim FJ. Dysregulated Cholinergic Signaling Inhibits Oligodendrocyte Maturation Following Demyelination. J Neurosci 2024; 44:e0051242024. [PMID: 38749703 PMCID: PMC11236584 DOI: 10.1523/jneurosci.0051-24.2024] [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: 01/04/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 06/20/2024] Open
Abstract
Dysregulation of oligodendrocyte progenitor cell (OPC) recruitment and oligodendrocyte differentiation contribute to failure of remyelination in human demyelinating diseases such as multiple sclerosis (MS). Deletion of muscarinic receptor enhances OPC differentiation and remyelination. However, the role of ligand-dependent signaling versus constitutive receptor activation is unknown. We hypothesized that dysregulated acetylcholine (ACh) release upon demyelination contributes to ligand-mediated activation hindering myelin repair. Following chronic cuprizone (CPZ)-induced demyelination (male and female mice), we observed a 2.5-fold increase in ACh concentration. This increase in ACh concentration could be attributed to increased ACh synthesis or decreased acetylcholinesterase-/butyrylcholinesterase (BChE)-mediated degradation. Using choline acetyltransferase (ChAT) reporter mice, we identified increased ChAT-GFP expression following both lysolecithin and CPZ demyelination. ChAT-GFP expression was upregulated in a subset of injured and uninjured axons following intraspinal lysolecithin-induced demyelination. In CPZ-demyelinated corpus callosum, ChAT-GFP was observed in Gfap+ astrocytes and axons indicating the potential for neuronal and astrocytic ACh release. BChE expression was significantly decreased in the corpus callosum following CPZ demyelination. This decrease was due to the loss of myelinating oligodendrocytes which were the primary source of BChE. To determine the role of ligand-mediated muscarinic signaling following lysolecithin injection, we administered neostigmine, a cholinesterase inhibitor, to artificially raise ACh. We identified a dose-dependent decrease in mature oligodendrocyte density with no effect on OPC recruitment. Together, these results support a functional role of ligand-mediated activation of muscarinic receptors following demyelination and suggest that dysregulation of ACh homeostasis directly contributes to failure of remyelination in MS.
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Affiliation(s)
- Roopa Ravichandar
- Neuroscience Program, Jacob's School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203
| | - Farah Gadelkarim
- Neuroscience Program, Jacob's School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203
| | - Rupadevi Muthaiah
- Department of Pharmacology and Toxicology, Jacob's School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203
| | - Nicolas Glynos
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109
| | - Kateryna Murlanova
- Department of Physiology and Biophysics, Jacob's School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203
| | - Nagendra K Rai
- Department of Neuroscience, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio 44195
| | - Darpan Saraswat
- Department of Pharmacology and Toxicology, Jacob's School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203
| | - Jessie J Polanco
- Neuroscience Program, Jacob's School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203
| | - Ranjan Dutta
- Department of Neuroscience, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio 44195
| | - Dinesh Pal
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan 48109
| | - Fraser J Sim
- Neuroscience Program, Jacob's School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203
- Department of Pharmacology and Toxicology, Jacob's School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203
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18
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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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19
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Rodriguez-Rodriguez P, Arroyo-Garcia LE, Tsagkogianni C, Li L, Wang W, Végvári Á, Salas-Allende I, Plautz Z, Cedazo-Minguez A, Sinha SC, Troyanskaya O, Flajolet M, Yao V, Roussarie JP. A cell autonomous regulator of neuronal excitability modulates tau in Alzheimer's disease vulnerable neurons. Brain 2024; 147:2384-2399. [PMID: 38462574 PMCID: PMC11224620 DOI: 10.1093/brain/awae051] [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: 10/17/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 03/12/2024] Open
Abstract
Neurons from layer II of the entorhinal cortex (ECII) are the first to accumulate tau protein aggregates and degenerate during prodromal Alzheimer's disease. Gaining insight into the molecular mechanisms underlying this vulnerability will help reveal genes and pathways at play during incipient stages of the disease. Here, we use a data-driven functional genomics approach to model ECII neurons in silico and identify the proto-oncogene DEK as a regulator of tau pathology. We show that epigenetic changes caused by Dek silencing alter activity-induced transcription, with major effects on neuronal excitability. This is accompanied by the gradual accumulation of tau in the somatodendritic compartment of mouse ECII neurons in vivo, reactivity of surrounding microglia, and microglia-mediated neuron loss. These features are all characteristic of early Alzheimer's disease. The existence of a cell-autonomous mechanism linking Alzheimer's disease pathogenic mechanisms in the precise neuron type where the disease starts provides unique evidence that synaptic homeostasis dysregulation is of central importance in the onset of tau pathology in Alzheimer's disease.
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Affiliation(s)
| | | | - Christina Tsagkogianni
- Department of Neurobiology Care Sciences and Society, Karolinska Institutet, 17 164, Solna, Sweden
| | - Lechuan Li
- Department of Computer Science, Rice University, Houston, TX 77004, USA
| | - Wei Wang
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 164, Solna, Sweden
| | - Isabella Salas-Allende
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065, USA
| | - Zakary Plautz
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065, USA
| | - Angel Cedazo-Minguez
- Department of Neurobiology Care Sciences and Society, Karolinska Institutet, 17 164, Solna, Sweden
| | - Subhash C Sinha
- Helen and Robert Appel Alzheimer’s Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olga Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ 08540, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065, USA
| | - Vicky Yao
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 164, Solna, Sweden
| | - Jean-Pierre Roussarie
- Department of Anatomy & Neurobiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
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20
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Shwab EK, Gingerich DC, Man Z, Gamache J, Garrett ME, Crawford GE, Ashley-Koch AE, Serrano GE, Beach TG, Lutz MW, Chiba-Falek O. Single-nucleus multi-omics of Parkinson's disease reveals a glutamatergic neuronal subtype susceptible to gene dysregulation via alteration of transcriptional networks. Acta Neuropathol Commun 2024; 12:111. [PMID: 38956662 PMCID: PMC11218415 DOI: 10.1186/s40478-024-01803-1] [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: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
The genetic architecture of Parkinson's disease (PD) is complex and multiple brain cell subtypes are involved in the neuropathological progression of the disease. Here we aimed to advance our understanding of PD genetic complexity at a cell subtype precision level. Using parallel single-nucleus (sn)RNA-seq and snATAC-seq analyses we simultaneously profiled the transcriptomic and chromatin accessibility landscapes in temporal cortex tissues from 12 PD compared to 12 control subjects at a granular single cell resolution. An integrative bioinformatic pipeline was developed and applied for the analyses of these snMulti-omics datasets. The results identified a subpopulation of cortical glutamatergic excitatory neurons with remarkably altered gene expression in PD, including differentially-expressed genes within PD risk loci identified in genome-wide association studies (GWAS). This was the only neuronal subtype showing significant and robust overexpression of SNCA. Further characterization of this neuronal-subpopulation showed upregulation of specific pathways related to axon guidance, neurite outgrowth and post-synaptic structure, and downregulated pathways involved in presynaptic organization and calcium response. Additionally, we characterized the roles of three molecular mechanisms in governing PD-associated cell subtype-specific dysregulation of gene expression: (1) changes in cis-regulatory element accessibility to transcriptional machinery; (2) changes in the abundance of master transcriptional regulators, including YY1, SP3, and KLF16; (3) candidate regulatory variants in high linkage disequilibrium with PD-GWAS genomic variants impacting transcription factor binding affinities. To our knowledge, this study is the first and the most comprehensive interrogation of the multi-omics landscape of PD at a cell-subtype resolution. Our findings provide new insights into a precise glutamatergic neuronal cell subtype, causal genes, and non-coding regulatory variants underlying the neuropathological progression of PD, paving the way for the development of cell- and gene-targeted therapeutics to halt disease progression as well as genetic biomarkers for early preclinical diagnosis.
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Affiliation(s)
- E Keats Shwab
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Daniel C Gingerich
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Zhaohui Man
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Julia Gamache
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, 27701, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, 27708, USA
- Center for Advanced Genomic Technologies, Duke University Medical Center, Durham, NC, 27708, USA
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, 27701, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27708, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Michael W Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA.
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21
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Zeng Y, Ma Q, Chen J, Kong X, Chen Z, Liu H, Liu L, Qian Y, Wang X, Lu S. Single-cell sequencing: Current applications in various tuberculosis specimen types. Cell Prolif 2024:e13698. [PMID: 38956399 DOI: 10.1111/cpr.13698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/21/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
Tuberculosis (TB) is a chronic disease caused by Mycobacterium tuberculosis (M.tb) and responsible for millions of deaths worldwide each year. It has a complex pathogenesis that primarily affects the lungs but can also impact systemic organs. In recent years, single-cell sequencing technology has been utilized to characterize the composition and proportion of immune cell subpopulations associated with the pathogenesis of TB disease since it has a high resolution that surpasses conventional techniques. This paper reviews the current use of single-cell sequencing technologies in TB research and their application in analysing specimens from various sources of TB, primarily peripheral blood and lung specimens. The focus is on how these technologies can reveal dynamic changes in immune cell subpopulations, genes and proteins during disease progression after M.tb infection. Based on the current findings, single-cell sequencing has significant potential clinical value in the field of TB research. Next, we will focus on the real-world applications of the potential targets identified through single-cell sequencing for diagnostics, therapeutics and the development of effective vaccines.
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Affiliation(s)
- Yuqin Zeng
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Quan Ma
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Jinyun Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xingxing Kong
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Zhanpeng Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Huazhen Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Lanlan Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Yan Qian
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xiaomin Wang
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Shuihua Lu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
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22
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Patel Y, Woo A, Shi S, Ayoub R, Shin J, Botta A, Ketela T, Sung HK, Lerch J, Nieman B, Paus T, Pausova Z. Obesity and the cerebral cortex: Underlying neurobiology in mice and humans. Brain Behav Immun 2024; 119:637-647. [PMID: 38663773 DOI: 10.1016/j.bbi.2024.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024] Open
Abstract
Obesity is a major modifiable risk factor for Alzheimer's disease (AD), characterized by progressive atrophy of the cerebral cortex. The neurobiology of obesity contributions to AD is poorly understood. Here we show with in vivo MRI that diet-induced obesity decreases cortical volume in mice, and that higher body adiposity associates with lower cortical volume in humans. Single-nuclei transcriptomics of the mouse cortex reveals that dietary obesity promotes an array of neuron-adverse transcriptional dysregulations, which are mediated by an interplay of excitatory neurons and glial cells, and which involve microglial activation and lowered neuronal capacity for neuritogenesis and maintenance of membrane potential. The transcriptional dysregulations of microglia, more than of other cell types, are like those in AD, as assessed with single-nuclei cortical transcriptomics in a mouse model of AD and two sets of human donors with the disease. Serial two-photon tomography of microglia demonstrates microgliosis throughout the mouse cortex. The spatial pattern of adiposity-cortical volume associations in human cohorts interrogated together with in silico bulk and single-nucleus transcriptomic data from the human cortex implicated microglia (along with other glial cells and subtypes of excitatory neurons), and it correlated positively with the spatial profile of cortical atrophy in patients with mild cognitive impairment and AD. Thus, multi-cell neuron-adverse dysregulations likely contribute to the loss of cortical tissue in obesity. The dysregulations of microglia may be pivotal to the obesity-related risk of AD.
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Affiliation(s)
- Yash Patel
- The Hospital for Sick Children, Translational Medicine Program, Toronto, ON, Canada; Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada; Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Anita Woo
- The Hospital for Sick Children, Translational Medicine Program, Toronto, ON, Canada; Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Sammy Shi
- The Hospital for Sick Children, Translational Medicine Program, Toronto, ON, Canada; Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Ramy Ayoub
- The Hospital for Sick Children, Translational Medicine Program, Toronto, ON, Canada
| | - Jean Shin
- The Hospital for Sick Children, Translational Medicine Program, Toronto, ON, Canada; Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Amy Botta
- The Hospital for Sick Children, Translational Medicine Program, Toronto, ON, Canada
| | - Troy Ketela
- Princess Margaret Genomics Centre, Toronto, ON, Canada
| | - Hoon-Ki Sung
- The Hospital for Sick Children, Translational Medicine Program, Toronto, ON, Canada
| | - Jason Lerch
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, Great Britton
| | - Brian Nieman
- The Hospital for Sick Children, Translational Medicine Program, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Tomas Paus
- Department of Psychiatry and Addictology and Department of Neuroscience, Faculty of Medicine and Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, QC, Canada
| | - Zdenka Pausova
- The Hospital for Sick Children, Translational Medicine Program, Toronto, ON, Canada; Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada; Department of Pediatrics and Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, QC, Canada.
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23
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Butler CA, Mendoza Arvilla A, Milinkeviciute G, Da Cunha C, Kawauchi S, Rezaie N, Liang HY, Javonillo D, Thach A, Wang S, Collins S, Walker A, Shi K, Neumann J, Gomez‐Arboledas A, Henningfield CM, Hohsfield LA, Mapstone M, Tenner AJ, LaFerla FM, Mortazavi A, MacGregor GR, Green KN. The Abca7 V1613M variant reduces Aβ generation, plaque load, and neuronal damage. Alzheimers Dement 2024; 20:4914-4934. [PMID: 38506634 PMCID: PMC11247689 DOI: 10.1002/alz.13783] [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: 10/09/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 03/21/2024]
Abstract
BACKGROUND Variants in ABCA7, a member of the ABC transporter superfamily, have been associated with increased risk for developing late onset Alzheimer's disease (LOAD). METHODS CRISPR-Cas9 was used to generate an Abca7V1613M variant in mice, modeling the homologous human ABCA7V1599M variant, and extensive characterization was performed. RESULTS Abca7V1613M microglia show differential gene expression profiles upon lipopolysaccharide challenge and increased phagocytic capacity. Homozygous Abca7V1613M mice display elevated circulating cholesterol and altered brain lipid composition. When crossed with 5xFAD mice, homozygous Abca7V1613M mice display fewer Thioflavin S-positive plaques, decreased amyloid beta (Aβ) peptides, and altered amyloid precursor protein processing and trafficking. They also exhibit reduced Aβ-associated inflammation, gliosis, and neuronal damage. DISCUSSION Overall, homozygosity for the Abca7V1613M variant influences phagocytosis, response to inflammation, lipid metabolism, Aβ pathology, and neuronal damage in mice. This variant may confer a gain of function and offer a protective effect against Alzheimer's disease-related pathology. HIGHLIGHTS ABCA7 recognized as a top 10 risk gene for developing Alzheimer's disease. Loss of function mutations result in increased risk for LOAD. V1613M variant reduces amyloid beta plaque burden in 5xFAD mice. V1613M variant modulates APP processing and trafficking in 5xFAD mice. V1613M variant reduces amyloid beta-associated damage in 5xFAD mice.
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Affiliation(s)
- Claire A. Butler
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
| | - Adrian Mendoza Arvilla
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
| | - Giedre Milinkeviciute
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
| | - Celia Da Cunha
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
| | - Shimako Kawauchi
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
- Transgenic Mouse Facility, ULAR, Office of ResearchUniversity of CaliforniaIrvineCaliforniaUSA
| | - Narges Rezaie
- Department of Developmental and Cell BiologyUniversity of CaliforniaIrvineCaliforniaUSA
- Center for Complex Biological SystemsUniversity of CaliforniaIrvineCaliforniaUSA
| | - Heidi Y. Liang
- Department of Developmental and Cell BiologyUniversity of CaliforniaIrvineCaliforniaUSA
- Center for Complex Biological SystemsUniversity of CaliforniaIrvineCaliforniaUSA
| | - Dominic Javonillo
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
| | - Annie Thach
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
| | - Shuling Wang
- Transgenic Mouse Facility, ULAR, Office of ResearchUniversity of CaliforniaIrvineCaliforniaUSA
| | - Sherilyn Collins
- Transgenic Mouse Facility, ULAR, Office of ResearchUniversity of CaliforniaIrvineCaliforniaUSA
| | - Amber Walker
- Transgenic Mouse Facility, ULAR, Office of ResearchUniversity of CaliforniaIrvineCaliforniaUSA
| | - Kai‐Xuan Shi
- Transgenic Mouse Facility, ULAR, Office of ResearchUniversity of CaliforniaIrvineCaliforniaUSA
| | - Jonathan Neumann
- Transgenic Mouse Facility, ULAR, Office of ResearchUniversity of CaliforniaIrvineCaliforniaUSA
| | - Angela Gomez‐Arboledas
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
| | | | - Lindsay A. Hohsfield
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
| | - Mark Mapstone
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
- Department of NeurologyUniversity of CaliforniaIrvineCaliforniaUSA
| | - Andrea J. Tenner
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
- Department of Molecular Biology & BiochemistryUniversity of CaliforniaIrvineCaliforniaUSA
- Department of Pathology and Laboratory MedicineUniversity of CaliforniaIrvineCaliforniaUSA
| | - Frank M. LaFerla
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
| | - Ali Mortazavi
- Department of Developmental and Cell BiologyUniversity of CaliforniaIrvineCaliforniaUSA
- Center for Complex Biological SystemsUniversity of CaliforniaIrvineCaliforniaUSA
| | - Grant R. MacGregor
- Transgenic Mouse Facility, ULAR, Office of ResearchUniversity of CaliforniaIrvineCaliforniaUSA
- Department of Developmental and Cell BiologyUniversity of CaliforniaIrvineCaliforniaUSA
| | - Kim N. Green
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
- Institute for Memory Impairments and Neurological DisordersUniversity of CaliforniaIrvineCaliforniaUSA
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24
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Chang X, Zheng Y, Xu K. Single-Cell RNA Sequencing: Technological Progress and Biomedical Application in Cancer Research. Mol Biotechnol 2024; 66:1497-1519. [PMID: 37322261 PMCID: PMC11217094 DOI: 10.1007/s12033-023-00777-0] [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: 03/09/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023]
Abstract
Single-cell RNA-seq (scRNA-seq) is a revolutionary technology that allows for the genomic investigation of individual cells in a population, allowing for the discovery of unusual cells associated with cancer and metastasis. ScRNA-seq has been used to discover different types of cancers with poor prognosis and medication resistance such as lung cancer, breast cancer, ovarian cancer, and gastric cancer. Besides, scRNA-seq is a promising method that helps us comprehend the biological features and dynamics of cell development, as well as other disorders. This review gives a concise summary of current scRNA-seq technology. We also explain the main technological steps involved in implementing the technology. We highlight the present applications of scRNA-seq in cancer research, including tumor heterogeneity analysis in lung cancer, breast cancer, and ovarian cancer. In addition, this review elucidates potential applications of scRNA-seq in lineage tracing, personalized medicine, illness prediction, and disease diagnosis, which reveals that scRNA-seq facilitates these events by producing genetic variations on the single-cell level.
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Affiliation(s)
- Xu Chang
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Yunxi Zheng
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Kai Xu
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China.
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25
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Rajani RM, Ellingford R, Hellmuth M, Harris SS, Taso OS, Graykowski D, Lam FKW, Arber C, Fertan E, Danial JSH, Swire M, Lloyd M, Giovannucci TA, Bourdenx M, Klenerman D, Vassar R, Wray S, Sala Frigerio C, Busche MA. Selective suppression of oligodendrocyte-derived amyloid beta rescues neuronal dysfunction in Alzheimer's disease. PLoS Biol 2024; 22:e3002727. [PMID: 39042667 PMCID: PMC11265669 DOI: 10.1371/journal.pbio.3002727] [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: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/25/2024] Open
Abstract
Reduction of amyloid beta (Aβ) has been shown to be effective in treating Alzheimer's disease (AD), but the underlying assumption that neurons are the main source of pathogenic Aβ is untested. Here, we challenge this prevailing belief by demonstrating that oligodendrocytes are an important source of Aβ in the human brain and play a key role in promoting abnormal neuronal hyperactivity in an AD knock-in mouse model. We show that selectively suppressing oligodendrocyte Aβ production improves AD brain pathology and restores neuronal function in the mouse model in vivo. Our findings suggest that targeting oligodendrocyte Aβ production could be a promising therapeutic strategy for treating AD.
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Affiliation(s)
- Rikesh M. Rajani
- UK Dementia Research Institute at UCL, University College London, London, United Kingdom
| | - Robert Ellingford
- UK Dementia Research Institute at UCL, University College London, London, United Kingdom
| | - Mariam Hellmuth
- UK Dementia Research Institute at UCL, University College London, London, United Kingdom
| | - Samuel S. Harris
- UK Dementia Research Institute at UCL, University College London, London, United Kingdom
| | - Orjona S. Taso
- UK Dementia Research Institute at UCL, University College London, London, United Kingdom
| | - David Graykowski
- UK Dementia Research Institute at UCL, University College London, London, United Kingdom
| | - Francesca Kar Wey Lam
- UK Dementia Research Institute at UCL, University College London, London, United Kingdom
| | - Charles Arber
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, United Kingdom
| | - Emre Fertan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- UK Dementia Research Institute at University of Cambridge, Cambridge, United Kingdom
| | - John S. H. Danial
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- UK Dementia Research Institute at University of Cambridge, Cambridge, United Kingdom
- School of Physics and Astronomy, University of St Andrews, St. Andrews, United Kingdom
| | - Matthew Swire
- Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
| | - Marcus Lloyd
- Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
| | - Tatiana A. Giovannucci
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, United Kingdom
| | - Mathieu Bourdenx
- UK Dementia Research Institute at UCL, University College London, London, United Kingdom
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- UK Dementia Research Institute at University of Cambridge, Cambridge, United Kingdom
| | - Robert Vassar
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Selina Wray
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, United Kingdom
| | - Carlo Sala Frigerio
- UK Dementia Research Institute at UCL, University College London, London, United Kingdom
| | - Marc Aurel Busche
- UK Dementia Research Institute at UCL, University College London, London, United Kingdom
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26
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Limone F, Mordes DA, Couto A, Joseph BJ, Mitchell JM, Therrien M, Ghosh SD, Meyer D, Zhang Y, Goldman M, Bortolin L, Cobos I, Stevens B, McCarroll SA, Kadiu I, Burberry A, Pietiläinen O, Eggan K. Single-nucleus sequencing reveals enriched expression of genetic risk factors in extratelencephalic neurons sensitive to degeneration in ALS. NATURE AGING 2024; 4:984-997. [PMID: 38907103 PMCID: PMC11257952 DOI: 10.1038/s43587-024-00640-0] [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: 10/13/2022] [Accepted: 05/01/2024] [Indexed: 06/23/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by a progressive loss of motor function linked to degenerating extratelencephalic neurons/Betz cells (ETNs). The reasons why these neurons are selectively affected remain unclear. Here, to understand the unique molecular properties that may sensitize ETNs to ALS, we performed RNA sequencing of 79,169 single nuclei from cortices of patients and controls. In both patients and unaffected individuals, we found significantly higher expression of ALS risk genes in THY1+ ETNs, regardless of diagnosis. In patients, this was accompanied by the induction of genes involved in protein homeostasis and stress responses that were significantly induced in a wide collection of ETNs. Examination of oligodendroglial and microglial nuclei revealed patient-specific downregulation of myelinating genes in oligodendrocytes and upregulation of an endolysosomal reactive state in microglia. Our findings suggest that selective vulnerability of extratelencephalic neurons is partly connected to their intrinsic molecular properties sensitizing them to genetics and mechanisms of degeneration.
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Affiliation(s)
- Francesco Limone
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA.
| | - Daniel A Mordes
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Alexander Couto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Brian J Joseph
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Jana M Mitchell
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martine Therrien
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Sulagna Dia Ghosh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Yingying Zhang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Melissa Goldman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Laura Bortolin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Inma Cobos
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Beth Stevens
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Irena Kadiu
- Neuroinflammation Focus Area, UCB Pharma, Braine-l'Alleud, Belgium
| | - Aaron Burberry
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Olli Pietiläinen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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27
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Ma Y, Zhou X. Accurate and efficient integrative reference-informed spatial domain detection for spatial transcriptomics. Nat Methods 2024; 21:1231-1244. [PMID: 38844627 DOI: 10.1038/s41592-024-02284-9] [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: 05/10/2023] [Accepted: 04/18/2024] [Indexed: 06/23/2024]
Abstract
Spatially resolved transcriptomics (SRT) studies are becoming increasingly common and large, offering unprecedented opportunities in mapping complex tissue structures and functions. Here we present integrative and reference-informed tissue segmentation (IRIS), a computational method designed to characterize tissue spatial organization in SRT studies through accurately and efficiently detecting spatial domains. IRIS uniquely leverages single-cell RNA sequencing data for reference-informed detection of biologically interpretable spatial domains, integrating multiple SRT slices while explicitly considering correlations both within and across slices. We demonstrate the advantages of IRIS through in-depth analysis of six SRT datasets encompassing diverse technologies, tissues, species and resolutions. In these applications, IRIS achieves substantial accuracy gains (39-1,083%) and speed improvements (4.6-666.0) in moderate-sized datasets, while representing the only method applicable for large datasets including Stereo-seq and 10x Xenium. As a result, IRIS reveals intricate brain structures, uncovers tumor microenvironment heterogeneity and detects structural changes in diabetes-affected testis, all with exceptional speed and accuracy.
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Affiliation(s)
- Ying Ma
- Department of Biostatistics, Brown University, Providence, RI, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA.
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28
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Li K, Wang S, Luo X, Zeng Q, Liu X, Hong L, Li J, Hong H, Xu X, Zhang Y, Jiaerken Y, Zhang R, Xie L, Xu S, Zhang X, Chen Y, Liu Z, Zhang M, Huang P. Associations of Alzheimer's Disease Pathology and Small Vessel Disease With Cerebral White Matter Degeneration: A Tract-Based MR Diffusion Imaging Study. J Magn Reson Imaging 2024; 60:268-278. [PMID: 37737474 DOI: 10.1002/jmri.29022] [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: 06/04/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND White matter (WM) degeneration is a key feature of Alzheimer's disease (AD). However, the underlying mechanism remains unclear. PURPOSE To investigate how amyloid-β (Aβ), tau, and small vascular disease (SVD) jointly affect WM degeneration in subjects along AD continuum. STUDY TYPE Retrospective. SUBJECTS 152 non-demented participants (age: 55.8-91.6, male/female: 66/86) from the ADNI database were included, classified into three groups using the A (Aβ)/T (tau)/N pathological scheme (Group 1: A-T-; Group 2: A+T-; Group 3: A+T+) based on positron emission tomography data. FIELD STRENGTH/SEQUENCE 3T; T1-weighted images, T2-weighted fluid-attenuated inversion recovery images, T2*-weighted images, diffusion-weighted spin-echo echo-planar imaging sequence (54 diffusion directions). ASSESSMENT Free-water diffusion model (generated parameters: free water, FW; tissue fractional anisotropy, FAt; tissue mean diffusivity, MDt); SVD total score; Neuropsychological tests. STATISTICAL TESTS Linear regression analysis was performed to investigate the independent contribution of AD (Aβ and tau) and SVD pathologies to diffusion parameters in each fiber tract, first in the entire population and then in each subgroup. We also investigated associations between diffusion parameters and cognitive functions. The level of statistical significance was set at p < 0.05 (false discovery rate corrected). RESULTS In the entire population, we found that: 1) Increased FW was significantly associated with SVD and tau, while FAt and MDt were significantly associated with Aβ and tau; 2) The spatial pattern of fiber tracts related to a certain pathological marker is consistent with the known distribution of that pathology; 3) Subgroup analysis showed that Group 2 and 3 had more alterations of FAt and MDt associated with Aβ and tau; 4) Diffusion imaging indices showed significant associations with cognitive score in all domains except memory. DATA CONCLUSION WM microstructural injury was associated with both AD and SVD pathologies, showing compartment-specific, tract-specific, and stage-specific WM patterns. EVIDENCE LEVEL 1 TECHNICAL EFFICACY: Stage 3.
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Affiliation(s)
- Kaicheng Li
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Shuyue Wang
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao Luo
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Qingze Zeng
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaocao Liu
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Luwei Hong
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Jixuan Li
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Hong
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaopei Xu
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yao Zhang
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yeerfan Jiaerken
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Ruiting Zhang
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Linyun Xie
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Shan Xu
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyi Zhang
- Department of Neurology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yanxing Chen
- Department of Neurology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Zhirong Liu
- Department of Neurology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Minming Zhang
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Peiyu Huang
- Department of Radiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
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29
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Chen R, Nie P, Wang J, Wang GZ. Deciphering brain cellular and behavioral mechanisms: Insights from single-cell and spatial RNA sequencing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1865. [PMID: 38972934 DOI: 10.1002/wrna.1865] [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: 01/31/2024] [Revised: 05/05/2024] [Accepted: 05/14/2024] [Indexed: 07/09/2024]
Abstract
The brain is a complex computing system composed of a multitude of interacting neurons. The computational outputs of this system determine the behavior and perception of every individual. Each brain cell expresses thousands of genes that dictate the cell's function and physiological properties. Therefore, deciphering the molecular expression of each cell is of great significance for understanding its characteristics and role in brain function. Additionally, the positional information of each cell can provide crucial insights into their involvement in local brain circuits. In this review, we briefly overview the principles of single-cell RNA sequencing and spatial transcriptomics, the potential issues and challenges in their data processing, and their applications in brain research. We further outline several promising directions in neuroscience that could be integrated with single-cell RNA sequencing, including neurodevelopment, the identification of novel brain microstructures, cognition and behavior, neuronal cell positioning, molecules and cells related to advanced brain functions, sleep-wake cycles/circadian rhythms, and computational modeling of brain function. We believe that the deep integration of these directions with single-cell and spatial RNA sequencing can contribute significantly to understanding the roles of individual cells or cell types in these specific functions, thereby making important contributions to addressing critical questions in those fields. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA in Disease and Development > RNA in Development RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Renrui Chen
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Pengxing Nie
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jing Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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30
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Bodai L, Borosta R, Ferencz Á, Kovács M, Zsindely N. The Role of miR-137 in Neurodegenerative Disorders. Int J Mol Sci 2024; 25:7229. [PMID: 39000336 PMCID: PMC11241563 DOI: 10.3390/ijms25137229] [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: 05/30/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Neurodegenerative diseases affect an increasing part of the population of modern societies, burdening healthcare systems and causing immense suffering at the personal level. The pathogenesis of several of these disorders involves dysregulation of gene expression, which depends on several molecular processes ranging from transcription to protein stability. microRNAs (miRNAs) are short non-coding RNA molecules that modulate gene expression by suppressing the translation of partially complementary mRNAs. miR-137 is a conserved, neuronally enriched miRNA that is implicated in neurodegeneration. Here, we review the current body of knowledge about the role that miR-137 plays in five prominent neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and multiple sclerosis. The presented data indicate that, rather than having a general neuroprotective role, miR-137 modulates the pathology of distinct disorders differently.
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Affiliation(s)
- László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Roberta Borosta
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Ágnes Ferencz
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Mercédesz Kovács
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Nóra Zsindely
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Department of Genetics, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
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31
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Baghel MS, Burns GD, Tsapatsis M, Mallika AP, Cruz ALF, Cao T, Chen XK, Rosa IDL, Marx SR, Ye Y, Sun S, Li T, Wong PC. Depletion of TDP-43 exacerbates tauopathy-dependent brain atrophy by sensitizing vulnerable neurons to caspase 3-mediated endoproteolysis of tau in a mouse model of Multiple Etiology Dementia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600814. [PMID: 38979270 PMCID: PMC11230425 DOI: 10.1101/2024.06.26.600814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
TDP-43 proteinopathy, initially disclosed in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), coexists with tauopathy in a variety of neurodegenerative disorders, termed multiple etiology dementias (MEDs), including Alzheimer's Disease (AD). While such co-pathology of TDP-43 is strongly associated with worsened neurodegeneration and steeper cognitive decline, the pathogenic mechanism underlying the exacerbated neuron loss remains elusive. The loss of TDP-43 splicing repression that occurs in presymptomatic ALS-FTD individuals suggests that such early loss could facilitate the pathological conversion of tau to accelerate neuron loss. Here, we report that the loss of TDP-43 repression of cryptic exons in forebrain neurons (CaMKII-CreER;Tardbp f/f mice) is necessary to exacerbate tauopathy-dependent brain atrophy by sensitizing vulnerable neurons to caspase 3-dependent cleavage of endogenous tau to promote tauopathy. Corroborating this finding within the human context, we demonstrate that loss of TDP-43 function in iPSC-derived cortical neurons promotes early cryptic exon inclusion and subsequent caspase 3-mediated endoproteolysis of tau. Using a genetic approach to seed tauopathy in CaMKII-CreER;Tardbp f/f mice by expressing a four-repeat microtubule binding domain of human tau, we show that the amount of tau seed positively correlates with levels of caspase 3-cleaved tau. Importantly, we found that the vulnerability of hippocampal neurons to TDP-43 depletion is dependent on the amount of caspase 3-cleaved tau: from most vulnerable neurons in the CA2/3, followed by those in the dentate gyrus, to the least in CA1. Taken together, our findings strongly support the view that TDP-43 loss-of-function exacerbates tauopathy-dependent brain atrophy by increasing the sensitivity of vulnerable neurons to caspase 3-mediated endoproteolysis of tau, resulting in a greater degree of neurodegeneration in human disorders with co-pathologies of tau and TDP-43. Our work thus discloses novel mechanistic insights and therapeutic targets for human tauopathies harboring co-pathology of TDP-43 and provides a new MED model for testing therapeutic strategies.
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Affiliation(s)
- Meghraj S Baghel
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Grace D Burns
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Margarita Tsapatsis
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Aswathy Peethambaran Mallika
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Anna Lourdes F Cruz
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Tianyu Cao
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Xiaoke K Chen
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Isabel De La Rosa
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Shaelyn R Marx
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Yingzhi Ye
- Department of Physiology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Shuying Sun
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
- Department of Physiology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
- Department of Neuroscience, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Tong Li
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
| | - Philip C Wong
- Department of Pathology, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
- Department of Neuroscience, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 558, Baltimore, MD 21205, USA
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32
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Liu A, Citu C, Enduru N, Chen X, Manuel AM, Sinha T, Gorski D, Fernandes BS, Yu M, Schulz PE, Simon LM, Soto C, Zhao Z. Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600720. [PMID: 38979371 PMCID: PMC11230393 DOI: 10.1101/2024.06.25.600720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Sporadic early-onset Alzheimer's disease (sEOAD) represents a significant but less-studied subtype of Alzheimer's disease (AD). Here, we generated a single-nucleus multiome atlas derived from the postmortem prefrontal cortex, entorhinal cortex, and hippocampus of nine individuals with or without sEOAD. Comprehensive analyses were conducted to delineate cell type-specific transcriptomic changes and linked candidate cis- regulatory elements (cCREs) across brain regions. We prioritized seven conservative transcription factors in glial cells in multiple brain regions, including RFX4 in astrocytes and IKZF1 in microglia, which are implicated in regulating sEOAD-associated genes. Moreover, we identified the top 25 altered intercellular signaling between glial cells and neurons, highlighting their regulatory potential on gene expression in receiver cells. We reported 38 cCREs linked to sEOAD-associated genes overlapped with late-onset AD risk loci, and sEOAD cCREs enriched in neuropsychiatric disorder risk loci. This atlas helps dissect transcriptional and chromatin dynamics in sEOAD, providing a key resource for AD research.
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Cavagnero KJ, Albright J, Li F, Dokoshi T, Bogle R, Kirma J, Kahlenberg JM, Billi AC, Fox J, Coon A, Dobry CJ, Hinds B, Tsoi LC, Harms PW, Gudjonsson JE, Gallo RL. Positionally distinct interferon stimulated dermal immune acting fibroblasts promote neutrophil recruitment in Sweet's syndrome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600500. [PMID: 38979312 PMCID: PMC11230187 DOI: 10.1101/2024.06.24.600500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Sweet's syndrome is a poorly understood inflammatory skin disease characterized by neutrophil infiltration to the dermis. Single-nucleus and bulk transcriptomics of archival clinical samples of Sweet's syndrome revealed a prominent interferon signature in Sweet's syndrome skin that was reduced in tissue from other neutrophilic dermatoses. This signature was observed in different subsets of cells, including fibroblasts that expressed interferon-induced genes. Functionally, this response was supported by analysis of cultured primary human dermal fibroblasts that were observed to highly express neutrophil chemokines in response to activation by type I interferon. Furthermore, single-molecule resolution spatial transcriptomics of skin in Sweet's syndrome identified positionally distinct immune acting fibroblasts that included a CXCL1+ subset proximal to neutrophils and a CXCL12+ subset distal to the neutrophilic infiltrate. This study defines the cellular landscape of neutrophilic dermatoses and suggests dermal immune acting fibroblasts play a role in the pathogenesis of Sweet's syndrome through recognition of type I interferons.
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Affiliation(s)
| | - Julie Albright
- University of California, San Diego, Department of Dermatology
| | - Fengwu Li
- University of California, San Diego, Department of Dermatology
| | - Tatsuya Dokoshi
- University of California, San Diego, Department of Dermatology
| | | | - Joseph Kirma
- University of Michigan, Department of Dermatology
| | - J. Michelle Kahlenberg
- University of Michigan, Department of Dermatology
- University of Michigan, Department of Internal Medicine, Division of Rheumatology
- Taubman Medical Research Institute
| | - Allison C. Billi
- University of Michigan, Department of Dermatology
- Taubman Medical Research Institute
| | - Jennifer Fox
- University of Michigan, Department of Dermatology
| | - Anthony Coon
- University of Michigan, Department of Dermatology
| | | | - Brian Hinds
- University of California, San Diego, Department of Dermatology
| | - Lam C. Tsoi
- University of Michigan, Department of Dermatology
| | - Paul W. Harms
- University of Michigan, Department of Dermatology
- University of Michigan, Department of Pathology
| | - Johann E. Gudjonsson
- University of Michigan, Department of Dermatology
- University of Michigan, Department of Internal Medicine, Division of Rheumatology
- Taubman Medical Research Institute
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von Maydell D, Wright S, Bonner JM, Staab C, Spitaleri A, Liu L, Pao PC, Yu CJ, Scannail AN, Li M, Boix CA, Mathys H, Leclerc G, Menchaca GS, Welch G, Graziosi A, Leary N, Samaan G, Kellis M, Tsai LH. Single-cell atlas of ABCA7 loss-of-function reveals impaired neuronal respiration via choline-dependent lipid imbalances. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.05.556135. [PMID: 38979214 PMCID: PMC11230156 DOI: 10.1101/2023.09.05.556135] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Loss-of-function (LoF) variants in the lipid transporter ABCA7 significantly increase the risk of Alzheimer's disease (odds ratio ∼2), yet the pathogenic mechanisms and the neural cell types affected by these variants remain largely unknown. Here, we performed single-nuclear RNA sequencing of 36 human post-mortem samples from the prefrontal cortex of 12 ABCA7 LoF carriers and 24 matched non-carrier control individuals. ABCA7 LoF was associated with gene expression changes in all major cell types. Excitatory neurons, which expressed the highest levels of ABCA7, showed transcriptional changes related to lipid metabolism, mitochondrial function, cell cycle-related pathways, and synaptic signaling. ABCA7 LoF-associated transcriptional changes in neurons were similarly perturbed in carriers of the common AD missense variant ABCA7 p.Ala1527Gly (n = 240 controls, 135 carriers), indicating that findings from our study may extend to large portions of the at-risk population. Consistent with ABCA7's function as a lipid exporter, lipidomic analysis of isogenic iPSC-derived neurons (iNs) revealed profound intracellular triglyceride accumulation in ABCA7 LoF, which was accompanied by a relative decrease in phosphatidylcholine abundance. Metabolomic and biochemical analyses of iNs further indicated that ABCA7 LoF was associated with disrupted mitochondrial bioenergetics that suggested impaired lipid breakdown by uncoupled respiration. Treatment of ABCA7 LoF iNs with CDP-choline (a rate-limiting precursor of phosphatidylcholine synthesis) reduced triglyceride accumulation and restored mitochondrial function, indicating that ABCA7 LoF-induced phosphatidylcholine dyshomeostasis may directly disrupt mitochondrial metabolism of lipids. Treatment with CDP-choline also rescued intracellular amyloid β -42 levels in ABCA7 LoF iNs, further suggesting a link between ABCA7 LoF metabolic disruptions in neurons and AD pathology. This study provides a detailed transcriptomic atlas of ABCA7 LoF in the human brain and mechanistically links ABCA7 LoF-induced lipid perturbations to neuronal energy dyshomeostasis. In line with a growing body of evidence, our study highlights the central role of lipid metabolism in the etiology of Alzheimer's disease.
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Baumgartner A, Robinson M, Golde T, Jaydev S, Huang S, Hadlock J, Funk C. Fokker-Planck diffusion maps of multiple single cell microglial transcriptomes reveals radial differentiation into substates associated with Alzheimer's pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.599924. [PMID: 38979220 PMCID: PMC11230164 DOI: 10.1101/2024.06.21.599924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The identification of microglia subtypes is important for understanding the role of innate immunity in neurodegenerative diseases. Current methods of unsupervised cell type identification assume a small noise-to-signal ratio of transcriptome measurements that would produce well-separated cell clusters. However, identification of subtypes is obscured by gene expression noise, diminishing the distances in transcriptome space between distinct cell types and blurring boundaries. Here we use Fokker-Planck (FP) diffusion maps to model cellular differentiation as a stochastic process whereby cells settle into local minima, corresponding to cell subtypes, in a potential landscape constructed from transcriptome data using a nearest neighbor graph approach. By applying critical transition fields, we identify individual cells on the verge of transitioning between subtypes, revealing microglial cells in inactivated, homeostatic state before radially transitioning into various specialized subtypes. Specifically, we show that cells from Alzheimer's disease patients are enriched in a microglia subtype associated to antigen presentation and T-cell recruitment.
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Affiliation(s)
| | | | - Todd Golde
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Institute Emory Brain Health, Emory University School of Medicine, Atlanta, GA, USA
| | - Suman Jaydev
- Department of Neurology, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Sui Huang
- Institute for Systems Biology, Seattle, WA
| | - Jennifer Hadlock
- Institute for Systems Biology, Seattle, WA
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Cory Funk
- Institute for Systems Biology, Seattle, WA
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36
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Robertson KV, Rodriguez AS, Cartailler JP, Shrestha S, Schroeder KR, Valenti AM, Harrison FE, Hasty AH. Knockdown of microglial iron import gene, DMT1, worsens cognitive function and alters microglial transcriptional landscape in a sex-specific manner in the APP/PS1 model of Alzheimer's disease. RESEARCH SQUARE 2024:rs.3.rs-4559940. [PMID: 38978579 PMCID: PMC11230470 DOI: 10.21203/rs.3.rs-4559940/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Background Microglial cell iron load and inflammatory activation are significant hallmarks of late-stage Alzheimer's disease (AD). In vitro, microglia preferentially upregulate the iron importer, divalent metal transporter 1 (DMT1, gene name Slc11a2) in response to inflammatory stimuli, and excess iron can augment cellular inflammation, suggesting a feed-forward loop between iron import mechanisms and inflammatory signaling. However, it is not understood whether microglial iron import mechanisms directly contribute to inflammatory signaling and chronic disease in vivo. These studies determined the effects of microglial-specific knockdown of Slc11a2 on AD-related cognitive decline and microglial transcriptional phenotype. Methods In vitro experiments and RT-qPCR were used to assess a role for DMT1 in amyloid-β-associated inflammation. To determine the effects of microglial Slc11a2 knockdown on AD-related phenotypes in vivo, triple-transgenic Cx3cr1 Cre - ERT2 ;Slc11a2 flfl;APP/PS1 + or - mice were generated and administered corn oil or tamoxifen to induce knockdown at 5-6 months of age. Both sexes underwent behavioral analyses to assess cognition and memory (12-15 months of age). Hippocampal CD11b + microglia were magnetically isolated from female mice (15-17 months) and bulk RNA-sequencing analysis was conducted. Results DMT1 inhibition in vitro robustly decreased Aβ-induced inflammatory gene expression and cellular iron levels in conditions of excess iron. In vivo, Slc11a2 KD APP/PS1 female, but not male, mice displayed a significant worsening of memory function in Morris water maze and a fear conditioning assay, along with significant hyperactivity compared to control WT and APP/PS1 mice. Hippocampal microglia from Slc11a2 KD APP/PS1 females displayed significant increases in Enpp2, Ttr, and the iron-export gene, Slc40a1, compared to control APP/PS1 cells. Slc11a2 KD cells from APP/PS1 females also exhibited decreased expression of markers associated with disease-associated microglia (DAMs), such as Apoe, Ctsb, Csf1, and Hif1α. Conclusions This work suggests a sex-specific role for microglial iron import gene Slc11a2 in propagating behavioral and cognitive phenotypes in the APP/PS1 model of AD. These data also highlight an association between loss of a DAM-like phenotype in microglia and cognitive deficits in Slc11a2 KD APP/PS1 female mice. Overall, this work illuminates an iron-related pathway in microglia that may serve a protective role during disease and offers insight into mechanisms behind disease-related sex differences.
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Majumder M, Dutta D. Oligodendrocyte Dysfunction in Tauopathy: A Less Explored Area in Tau-Mediated Neurodegeneration. Cells 2024; 13:1112. [PMID: 38994964 PMCID: PMC11240328 DOI: 10.3390/cells13131112] [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: 06/05/2024] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 07/13/2024] Open
Abstract
Aggregation of the microtubule-associated protein tau (MAPT) is the hallmark pathology in a spectrum of neurodegenerative disorders collectively called tauopathies. Physiologically, tau is an inherent neuronal protein that plays an important role in the assembly of microtubules and axonal transport. However, disease-associated mutations of this protein reduce its binding to the microtubule components and promote self-aggregation, leading to formation of tangles in neurons. Tau is also expressed in oligodendrocytes, where it has significant developmental roles in oligodendrocyte maturation and myelin synthesis. Oligodendrocyte-specific tau pathology, in the form of fibrils and coiled coils, is evident in major tauopathies including progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), and Pick's disease (PiD). Multiple animal models of tauopathy expressing mutant forms of MAPT recapitulate oligodendroglial tau inclusions with potential to cause degeneration/malfunction of oligodendrocytes and affecting the neuronal myelin sheath. Till now, mechanistic studies heavily concentrated on elucidating neuronal tau pathology. Therefore, more investigations are warranted to comprehensively address tau-induced pathologies in oligodendrocytes. The present review provides the current knowledge available in the literature about the intricate relations between tau and oligodendrocytes in health and diseases.
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Affiliation(s)
- Moumita Majumder
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Debashis Dutta
- Department of Pediatrics, Darby’s Children Research Institute, Medical University of South Carolina, Charleston, SC 29425, USA
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Kedia S, Ji H, Feng R, Androvic P, Spieth L, Liu L, Franz J, Zdiarstek H, Anderson KP, Kaboglu C, Liu Q, Mattugini N, Cherif F, Prtvar D, Cantuti-Castelvetri L, Liesz A, Schifferer M, Stadelmann C, Tahirovic S, Gokce O, Simons M. T cell-mediated microglial activation triggers myelin pathology in a mouse model of amyloidosis. Nat Neurosci 2024:10.1038/s41593-024-01682-8. [PMID: 38937583 DOI: 10.1038/s41593-024-01682-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 05/14/2024] [Indexed: 06/29/2024]
Abstract
Age-related myelin damage induces inflammatory responses, yet its involvement in Alzheimer's disease remains uncertain, despite age being a major risk factor. Using a mouse model of Alzheimer's disease, we found that amyloidosis itself triggers age-related oligodendrocyte and myelin damage. Mechanistically, CD8+ T cells promote the progressive accumulation of abnormally interferon-activated microglia that display myelin-damaging activity. Thus, our data suggest that immune responses against myelinating oligodendrocytes may contribute to neurodegenerative diseases with amyloidosis.
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Affiliation(s)
- Shreeya Kedia
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Hao Ji
- Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, Munich, Germany
| | - Ruoqing Feng
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Peter Androvic
- Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, Munich, Germany
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
| | - Lena Spieth
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Lu Liu
- Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, Munich, Germany
| | - Jonas Franz
- Department of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
| | - Hanna Zdiarstek
- Department of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
| | - Katrin Perez Anderson
- Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, Munich, Germany
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
| | - Cem Kaboglu
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
- Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, Munich, Germany
| | - Qian Liu
- Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, Munich, Germany
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
| | - Nicola Mattugini
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Fatma Cherif
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Danilo Prtvar
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Ludovico Cantuti-Castelvetri
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Arthur Liesz
- Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Martina Schifferer
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Christine Stadelmann
- Department of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
| | - Sabina Tahirovic
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Ozgun Gokce
- Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, Munich, Germany
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Mikael Simons
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.
- Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, Munich, Germany.
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany.
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Bohannon DG, Long D, Okhravi HR, Lee SC, De Jesus CL, Neubert TA, Rostagno AA, Ghiso JA, Kim WK. Functionally distinct pericyte subsets differently regulate amyloid-β deposition in patients with Alzheimer's disease. Brain Pathol 2024:e13282. [PMID: 38932696 DOI: 10.1111/bpa.13282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Although the concept that the blood-brain barrier (BBB) plays an important role in the etiology and pathogenesis of Alzheimer's disease (AD) has become increasingly accepted, little is known yet about how it actually contributes. We and others have recently identified a novel functionally distinct subset of BBB pericytes (PCs). In the present study, we sought to determine whether these PC subsets differentially contribute to AD-associated pathologies by immunohistochemistry and amyloid beta (Aβ) peptidomics. We demonstrated that a disease-associated PC subset (PC2) expanded in AD patients compared to age-matched, cognitively unimpaired controls. Surprisingly, we found that this increase in the percentage of PC2 (%PC2) was correlated negatively with BBB breakdown in AD patients, unlike in natural aging or other reported disease conditions. The higher %PC2 in AD patients was also correlated with a lower Aβ42 plaque load and a lower Aβ42:Aβ40 ratio in the brain as determined by immunohistochemistry. Colocalization analysis of multicolor confocal immunofluorescence microscopy images suggests that AD patient with low %PC2 have higher BBB breakdown due to internalization of Aβ42 by the physiologically normal PC subset (PC1) and their concomitant cell death leading to more vessels without PCs and increased plaque load. On the contrary, it appears that PC2 can secrete cathepsin D to cleave and degrade Aβ built up outside of PC2 into more soluble forms, ultimately contributing to less BBB breakdown and reducing Aβ plaque load. Collectively our data shows functionally distinct mechanisms for PC1 and PC2 in high Aβ conditions, demonstrating the importance of correctly identifying these populations when investigating the contribution of neurovascular dysfunction to AD pathogenesis.
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Affiliation(s)
- Diana G Bohannon
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Danielle Long
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Hamid R Okhravi
- Glennan Center for Geriatrics and Gerontology, Eastern Virginia Medical School, Norfolk, Virginia, USA
- Integrated Neurodegenerative Disorders Center, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Sunhee C Lee
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | | | - Thomas A Neubert
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Agueda A Rostagno
- Department of Pathology, New York University Grossman School of Medicine, New York, New York, USA
| | - Jorge A Ghiso
- Department of Pathology, New York University Grossman School of Medicine, New York, New York, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, New York, USA
| | - Woong-Ki Kim
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia, USA
- Integrated Neurodegenerative Disorders Center, Eastern Virginia Medical School, Norfolk, Virginia, USA
- Division of Microbiology, Tulane National Primate Research Center, Covington, Louisiana, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
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Qu W, Lam M, McInvale JJ, Mares JA, Kwon S, Humala N, Mahajan A, Nguyen T, Jakubiak KA, Mun JY, Tedesco TG, Al-Dalahmah O, Hussaini SA, Sproul AA, Siegelin MD, De Jager PL, Canoll P, Menon V, Hargus G. Xenografted human iPSC-derived neurons with the familial Alzheimer's disease APP V717I mutation reveal dysregulated transcriptome signatures linked to synaptic function and implicate LINGO2 as a disease signaling mediator. Acta Neuropathol 2024; 147:107. [PMID: 38918213 PMCID: PMC11199265 DOI: 10.1007/s00401-024-02755-5] [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: 11/09/2023] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia, and disease mechanisms are still not fully understood. Here, we explored pathological changes in human induced pluripotent stem cell (iPSC)-derived neurons carrying the familial AD APPV717I mutation after cell injection into the mouse forebrain. APPV717I mutant iPSCs and isogenic controls were differentiated into neurons revealing enhanced Aβ42 production, elevated phospho-tau, and impaired neurite outgrowth in APPV717I neurons. Two months after transplantation, APPV717I and control neural cells showed robust engraftment but at 12 months post-injection, APPV717I grafts were smaller and demonstrated impaired neurite outgrowth compared to controls, while plaque and tangle pathology were not seen. Single-nucleus RNA-sequencing of micro-dissected grafts, performed 2 months after cell injection, identified significantly altered transcriptome signatures in APPV717I iPSC-derived neurons pointing towards dysregulated synaptic function and axon guidance. Interestingly, APPV717I neurons showed an increased expression of genes, many of which are also upregulated in postmortem neurons of AD patients including the transmembrane protein LINGO2. Downregulation of LINGO2 in cultured APPV717I neurons rescued neurite outgrowth deficits and reversed key AD-associated transcriptional changes related but not limited to synaptic function, apoptosis and cellular senescence. These results provide important insights into transcriptional dysregulation in xenografted APPV717I neurons linked to synaptic function, and they indicate that LINGO2 may represent a potential therapeutic target in AD.
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Affiliation(s)
- Wenhui Qu
- Department of Pathology and Cell Biology, Presbyterian Hospital, Columbia University, 650W 168th Street, New York, NY, USA
| | - Matti Lam
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Neurological Institute, Columbia University, 710 West 168th Street, New York, NY, USA
| | - Julie J McInvale
- Department of Pathology and Cell Biology, Presbyterian Hospital, Columbia University, 650W 168th Street, New York, NY, USA
| | - Jason A Mares
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Neurological Institute, Columbia University, 710 West 168th Street, New York, NY, USA
| | - Sam Kwon
- Department of Pathology and Cell Biology, Presbyterian Hospital, Columbia University, 650W 168th Street, New York, NY, USA
| | - Nelson Humala
- Department of Neurosurgery, Columbia University, New York, NY, USA
| | - Aayushi Mahajan
- Department of Neurosurgery, Columbia University, New York, NY, USA
| | - Trang Nguyen
- Department of Pathology and Cell Biology, Presbyterian Hospital, Columbia University, 650W 168th Street, New York, NY, USA
| | - Kelly A Jakubiak
- Department of Pathology and Cell Biology, Presbyterian Hospital, Columbia University, 650W 168th Street, New York, NY, USA
| | - Jeong-Yeon Mun
- Department of Pathology and Cell Biology, Presbyterian Hospital, Columbia University, 650W 168th Street, New York, NY, USA
| | - Thomas G Tedesco
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Osama Al-Dalahmah
- Department of Pathology and Cell Biology, Presbyterian Hospital, Columbia University, 650W 168th Street, New York, NY, USA
| | - Syed A Hussaini
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Andrew A Sproul
- Department of Pathology and Cell Biology, Presbyterian Hospital, Columbia University, 650W 168th Street, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Markus D Siegelin
- Department of Pathology and Cell Biology, Presbyterian Hospital, Columbia University, 650W 168th Street, New York, NY, USA
| | - Philip L De Jager
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Neurological Institute, Columbia University, 710 West 168th Street, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Presbyterian Hospital, Columbia University, 650W 168th Street, New York, NY, USA
| | - Vilas Menon
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Neurological Institute, Columbia University, 710 West 168th Street, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA.
| | - Gunnar Hargus
- Department of Pathology and Cell Biology, Presbyterian Hospital, Columbia University, 650W 168th Street, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA.
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Meadows SM, Palaguachi F, Jang MW, Licht-Murava A, Barnett D, Zimmer TS, Zhou C, McDonough SR, Orr AL, Orr AG. Hippocampal astrocytes induce sex-dimorphic effects on memory. Cell Rep 2024; 43:114278. [PMID: 38795347 PMCID: PMC11234507 DOI: 10.1016/j.celrep.2024.114278] [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: 10/27/2023] [Revised: 03/19/2024] [Accepted: 05/09/2024] [Indexed: 05/27/2024] Open
Abstract
Astrocytic receptors influence cognitive function and can promote behavioral deficits in disease. These effects may vary based on variables such as biological sex, but it is not known if the effects of astrocytic receptors are dependent on sex. We leveraged in vivo gene editing and chemogenetics to examine the roles of astrocytic receptors in spatial memory and other processes. We show that reductions in metabotropic glutamate receptor 3 (mGluR3), the main astrocytic glutamate receptor in adults, impair memory in females but enhance memory in males. Similarly, increases in astrocytic mGluR3 levels have sex-dependent effects and enhance memory in females. mGluR3 manipulations also alter spatial search strategies during recall in a sex-specific manner. In addition, acute chemogenetic stimulation of Gi/o-coupled or Gs-coupled receptors in hippocampal astrocytes induces bidirectional and sex-dimorphic effects on memory. Thus, astrocytes are sex-dependent modulators of cognitive function and may promote sex differences in aging and disease.
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Affiliation(s)
- Samantha M Meadows
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY 10021, USA
| | - Fernando Palaguachi
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Minwoo Wendy Jang
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Avital Licht-Murava
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Daniel Barnett
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY 10021, USA
| | - Till S Zimmer
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Constance Zhou
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
| | - Samantha R McDonough
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY 10021, USA
| | - Adam L Orr
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY 10021, USA
| | - Anna G Orr
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY 10021, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA.
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Jackson RJ, Hyman BT, Serrano-Pozo A. Multifaceted roles of APOE in Alzheimer disease. Nat Rev Neurol 2024:10.1038/s41582-024-00988-2. [PMID: 38906999 DOI: 10.1038/s41582-024-00988-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2024] [Indexed: 06/23/2024]
Abstract
For the past three decades, apolipoprotein E (APOE) has been known as the single greatest genetic modulator of sporadic Alzheimer disease (AD) risk, influencing both the average age of onset and the lifetime risk of developing AD. The APOEε4 allele significantly increases AD risk, whereas the ε2 allele is protective relative to the most common ε3 allele. However, large differences in effect size exist across ethnoracial groups that are likely to depend on both global genetic ancestry and local genetic ancestry, as well as gene-environment interactions. Although early studies linked APOE to amyloid-β - one of the two culprit aggregation-prone proteins that define AD - in the past decade, mounting work has associated APOE with other neurodegenerative proteinopathies and broader ageing-related brain changes, such as neuroinflammation, energy metabolism failure, loss of myelin integrity and increased blood-brain barrier permeability, with potential implications for longevity and resilience to pathological protein aggregates. Novel mouse models and other technological advances have also enabled a number of therapeutic approaches aimed at either attenuating the APOEε4-linked increased AD risk or enhancing the APOEε2-linked AD protection. This Review summarizes this progress and highlights areas for future research towards the development of APOE-directed therapeutics.
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Affiliation(s)
- Rosemary J Jackson
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Massachusetts Alzheimer's Disease Research Center, Charlestown, MA, USA.
| | - Alberto Serrano-Pozo
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Massachusetts Alzheimer's Disease Research Center, Charlestown, MA, USA.
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Sahelijo N, Rajagopalan P, Qian L, Rahman R, Priyadarshi D, Goldstein D, Thomopoulos SI, Bennett DA, Farrer LA, Stein TD, Shen L, Huang H, Nho K, Andrew SJ, Davatzikos C, Thompson PM, Tcw J, Jun GR. Brain Cell-based Genetic Subtyping and Drug Repositioning for Alzheimer Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.21.24309255. [PMID: 38947056 PMCID: PMC11213108 DOI: 10.1101/2024.06.21.24309255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Alzheimer's Disease (AD) is characterized by its complex and heterogeneous etiology and gradual progression, leading to high drug failure rates in late-stage clinical trials. In order to better stratify individuals at risk for AD and discern potential therapeutic targets we employed a novel procedure utilizing cell-based co-regulated gene networks and polygenic risk scores (cbPRSs). After defining genetic subtypes using extremes of cbPRS distributions, we evaluated correlations of the genetic subtypes with previously defined AD subtypes defined on the basis of domain-specific cognitive functioning and neuroimaging biomarkers. Employing a PageRank algorithm, we identified priority gene targets for the genetic subtypes. Pathway analysis of priority genes demonstrated associations with neurodegeneration and suggested candidate drugs currently utilized in diabetes, hypertension, and epilepsy for repositioning in AD. Experimental validation utilizing human induced pluripotent stem cell (hiPSC)-derived astrocytes demonstrated the modifying effects of estradiol, levetiracetam, and pioglitazone on expression of APOE and complement C4 genes, suggesting potential repositioning for AD.
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Choi JJ, Svaren J, Wang D. Single-cell multi-omics analysis reveals cooperative transcription factors for gene regulation in oligodendrocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599799. [PMID: 38948852 PMCID: PMC11213031 DOI: 10.1101/2024.06.19.599799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Oligodendrocytes are the myelinating cells within the central nervous system. Many oligodendrocyte genes have been associated with brain disorders. However, how transcription factors (TFs) cooperate for gene regulation in oligodendrocytes remains largely uncharacterized. To address this, we integrated scRNA-seq and scATAC-seq data to identify the cooperative TFs that co-regulate the target gene (TG) expression in oligodendrocytes. First, we identified co- binding TF pairs whose binding sites overlapped in oligodendrocyte-specific regulatory regions. Second, we trained a deep learning model to predict the expression level of each TG using the expression levels of co-binding TFs. Third, using the trained models, we computed the TF importance and TF-TF interaction scores for predicting TG expression by the Shapley interaction scores. We found that the co-binding TF pairs involving known important TF pairs for oligodendrocyte differentiation, such as SOX10-TCF12, SOX10-MYRF, and SOX10-OLIG2, exhibited significantly higher Shapley scores than others (t-test, p-value < 1e-4). Furthermore, we identified 153 oligodendrocyte-associated eQTLs that reside in oligodendrocyte-specific enhancers or promoters where their eGenes (TGs) are regulated by cooperative TFs, suggesting potential novel regulatory roles from genetic variants. We also experimentally validated some identified TF pairs such as SOX10-OLIG2 and SOX10-NKX2.2 by co-enrichment analysis, using ChIP-seq data from rat peripheral nerve.
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Adeoye T, Shah SI, Ullah G. Systematic Analysis of Biological Processes Reveals Gene Co-expression Modules Driving Pathway Dysregulation in Alzheimer's Disease. Aging Dis 2024:AD.2024.0429. [PMID: 38913039 DOI: 10.14336/ad.2024.0429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/12/2024] [Indexed: 06/25/2024] Open
Abstract
Alzheimer's disease (AD) manifests as a complex systems pathology with intricate interplay among various genes and biological processes. Traditional differential gene expression (DEG) analysis, while commonly employed to characterize AD-driven perturbations, does not sufficiently capture the full spectrum of underlying biological processes. Utilizing single-nucleus RNA-sequencing data from postmortem brain samples across key regions-middle temporal gyrus, superior frontal gyrus, and entorhinal cortex-we provide a comprehensive systematic analysis of disrupted processes in AD. We go beyond the DEG-centric analysis by integrating pathway activity analysis with weighted gene co-expression patterns to comprehensively map gene interconnectivity, identifying region- and cell-type-specific drivers of biological processes associated with AD. Our analysis reveals profound modular heterogeneity in neurons and glia as well as extensive AD-related functional disruptions. Co-expression networks highlighted the extended involvement of astrocytes and microglia in biological processes beyond neuroinflammation, such as calcium homeostasis, glutamate regulation, lipid metabolism, vesicle-mediated transport, and TOR signaling. We find limited representation of DEGs within dysregulated pathways across neurons and glial cells, suggesting that differential gene expression alone may not adequately represent the disease complexity. Further dissection of inferred gene modules revealed distinct dynamics of hub DEGs in neurons versus glia, suggesting that DEGs exert more impact on neurons compared to glial cells in driving modular dysregulations underlying perturbed biological processes. Interestingly, we observe an overall downregulation of astrocyte and microglia modules across all brain regions in AD, indicating a prevailing trend of functional repression in glial cells across these regions. Notable genes from the CALM and HSP90 families emerged as hub genes across neuronal modules in all brain regions, suggesting conserved roles as drivers of synaptic dysfunction in AD. Our findings demonstrate the importance of an integrated, systems-oriented approach combining pathway and network analysis to comprehensively understand the cell-type-specific roles of genes in AD-related biological processes.
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Jong Huat T, Camats-Perna J, Newcombe EA, Onraet T, Campbell D, Sucic JT, Martini A, Forner S, Mirzaei M, Poon W, LaFerla FM, Medeiros R. The impact of astrocytic NF-κB on healthy and Alzheimer's disease brains. Sci Rep 2024; 14:14305. [PMID: 38906984 PMCID: PMC11192733 DOI: 10.1038/s41598-024-65248-1] [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: 01/04/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024] Open
Abstract
Astrocytes play a role in healthy cognitive function and Alzheimer's disease (AD). The transcriptional factor nuclear factor-κB (NF-κB) drives astrocyte diversity, but the mechanisms are not fully understood. By combining studies in human brains and animal models and selectively manipulating NF-κB function in astrocytes, we deepened the understanding of the role of astrocytic NF-κB in brain health and AD. In silico analysis of bulk and cell-specific transcriptomic data revealed the association of NF-κB and astrocytes in AD. Confocal studies validated the higher level of p50 NF-κB and phosphorylated-p65 NF-κB in glial fibrillary acidic protein (GFAP)+-astrocytes in AD versus non-AD subjects. In the healthy mouse brain, chronic activation of astrocytic NF-κB disturbed the proteomic milieu, causing a loss of mitochondrial-associated proteins and the rise of inflammatory-related proteins. Sustained NF-κB signaling also led to microglial reactivity, production of pro-inflammatory mediators, and buildup of senescence-related protein p16INK4A in neurons. However, in an AD mouse model, NF-κB inhibition accelerated β-amyloid and tau accumulation. Molecular biology studies revealed that astrocytic NF-κB activation drives the increase in GFAP and inflammatory proteins and aquaporin-4, a glymphatic system protein that assists in mitigating AD. Our investigation uncovered fundamental mechanisms by which NF-κB enables astrocytes' neuroprotective and neurotoxic responses in the brain.
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Affiliation(s)
- Tee Jong Huat
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Centre for Stem Cell Ageing and Regenerative Engineering, The University of Queensland, Brisbane, QLD, Australia
| | - Judith Camats-Perna
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Estella A Newcombe
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Tessa Onraet
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Daniel Campbell
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Josiah T Sucic
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Alessandra Martini
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, 3400A Biological Sciences III, Irvine, CA, 92697-4545, USA
| | - Stefânia Forner
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, 3400A Biological Sciences III, Irvine, CA, 92697-4545, USA
| | - Mehdi Mirzaei
- Clinical Medicine Department, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Wayne Poon
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, 3400A Biological Sciences III, Irvine, CA, 92697-4545, USA
| | - Frank M LaFerla
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, 3400A Biological Sciences III, Irvine, CA, 92697-4545, USA
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
| | - Rodrigo Medeiros
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, 3400A Biological Sciences III, Irvine, CA, 92697-4545, USA.
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İş Ö, Wang X, Reddy JS, Min Y, Yilmaz E, Bhattarai P, Patel T, Bergman J, Quicksall Z, Heckman MG, Tutor-New FQ, Can Demirdogen B, White L, Koga S, Krause V, Inoue Y, Kanekiyo T, Cosacak MI, Nelson N, Lee AJ, Vardarajan B, Mayeux R, Kouri N, Deniz K, Carnwath T, Oatman SR, Lewis-Tuffin LJ, Nguyen T, Carrasquillo MM, Graff-Radford J, Petersen RC, Jr Jack CR, Kantarci K, Murray ME, Nho K, Saykin AJ, Dickson DW, Kizil C, Allen M, Ertekin-Taner N. Gliovascular transcriptional perturbations in Alzheimer's disease reveal molecular mechanisms of blood brain barrier dysfunction. Nat Commun 2024; 15:4758. [PMID: 38902234 PMCID: PMC11190273 DOI: 10.1038/s41467-024-48926-6] [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: 10/09/2023] [Accepted: 05/17/2024] [Indexed: 06/22/2024] Open
Abstract
To uncover molecular changes underlying blood-brain-barrier dysfunction in Alzheimer's disease, we performed single nucleus RNA sequencing in 24 Alzheimer's disease and control brains and focused on vascular and astrocyte clusters as main cell types of blood-brain-barrier gliovascular-unit. The majority of the vascular transcriptional changes were in pericytes. Of the vascular molecular targets predicted to interact with astrocytic ligands, SMAD3, upregulated in Alzheimer's disease pericytes, has the highest number of ligands including VEGFA, downregulated in Alzheimer's disease astrocytes. We validated these findings with external datasets comprising 4,730 pericyte and 150,664 astrocyte nuclei. Blood SMAD3 levels are associated with Alzheimer's disease-related neuroimaging outcomes. We determined inverse relationships between pericytic SMAD3 and astrocytic VEGFA in human iPSC and zebrafish models. Here, we detect vast transcriptome changes in Alzheimer's disease at the gliovascular-unit, prioritize perturbed pericytic SMAD3-astrocytic VEGFA interactions, and validate these in cross-species models to provide a molecular mechanism of blood-brain-barrier disintegrity in Alzheimer's disease.
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Affiliation(s)
- Özkan İş
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Joseph S Reddy
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Yuhao Min
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Elanur Yilmaz
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Prabesh Bhattarai
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Tulsi Patel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Zachary Quicksall
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Michael G Heckman
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | | | - Birsen Can Demirdogen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Launia White
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Shunsuke Koga
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Vincent Krause
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yasuteru Inoue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Mehmet Ilyas Cosacak
- German Center for Neurodegenerative Diseases (DZNE) within Helmholtz Association, Dresden, Germany
| | - Nastasia Nelson
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Annie J Lee
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Badri Vardarajan
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Richard Mayeux
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Naomi Kouri
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Kaancan Deniz
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Troy Carnwath
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Laura J Lewis-Tuffin
- Mayo Clinic Florida Cytometry and Cell Imaging Laboratory, Mayo Clinic, Jacksonville, FL, USA
| | - Thuy Nguyen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Ronald C Petersen
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Alzheimer's Disease Research Center, Rochester, MN, USA
| | | | - Kejal Kantarci
- Mayo Clinic Alzheimer's Disease Research Center, Rochester, MN, USA
| | | | - Kwangsik Nho
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Caghan Kizil
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
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Ament SA, Campbell RR, Lobo MK, Receveur JP, Agrawal K, Borjabad A, Byrareddy SN, Chang L, Clarke D, Emani P, Gabuzda D, Gaulton KJ, Giglio M, Giorgi FM, Gok B, Guda C, Hadas E, Herb BR, Hu W, Huttner A, Ishmam MR, Jacobs MM, Kelschenbach J, Kim DW, Lee C, Liu S, Liu X, Madras BK, Mahurkar AA, Mash DC, Mukamel EA, Niu M, O'Connor RM, Pagan CM, Pang APS, Pillai P, Repunte-Canonigo V, Ruzicka WB, Stanley J, Tickle T, Tsai SYA, Wang A, Wills L, Wilson AM, Wright SN, Xu S, Yang J, Zand M, Zhang L, Zhang J, Akbarian S, Buch S, Cheng CS, Corley MJ, Fox HS, Gerstein M, Gummuluru S, Heiman M, Ho YC, Kellis M, Kenny PJ, Kluger Y, Milner TA, Moore DJ, Morgello S, Ndhlovu LC, Rana TM, Sanna PP, Satterlee JS, Sestan N, Spector SA, Spudich S, Tilgner HU, Volsky DJ, White OR, Williams DW, Zeng H. The single-cell opioid responses in the context of HIV (SCORCH) consortium. Mol Psychiatry 2024:10.1038/s41380-024-02620-7. [PMID: 38879719 DOI: 10.1038/s41380-024-02620-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 05/12/2024] [Accepted: 05/17/2024] [Indexed: 06/19/2024]
Abstract
Substance use disorders (SUD) and drug addiction are major threats to public health, impacting not only the millions of individuals struggling with SUD, but also surrounding families and communities. One of the seminal challenges in treating and studying addiction in human populations is the high prevalence of co-morbid conditions, including an increased risk of contracting a human immunodeficiency virus (HIV) infection. Of the ~15 million people who inject drugs globally, 17% are persons with HIV. Conversely, HIV is a risk factor for SUD because chronic pain syndromes, often encountered in persons with HIV, can lead to an increased use of opioid pain medications that in turn can increase the risk for opioid addiction. We hypothesize that SUD and HIV exert shared effects on brain cell types, including adaptations related to neuroplasticity, neurodegeneration, and neuroinflammation. Basic research is needed to refine our understanding of these affected cell types and adaptations. Studying the effects of SUD in the context of HIV at the single-cell level represents a compelling strategy to understand the reciprocal interactions among both conditions, made feasible by the availability of large, extensively-phenotyped human brain tissue collections that have been amassed by the Neuro-HIV research community. In addition, sophisticated animal models that have been developed for both conditions provide a means to precisely evaluate specific exposures and stages of disease. We propose that single-cell genomics is a uniquely powerful technology to characterize the effects of SUD and HIV in the brain, integrating data from human cohorts and animal models. We have formed the Single-Cell Opioid Responses in the Context of HIV (SCORCH) consortium to carry out this strategy.
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Affiliation(s)
- Seth A Ament
- University of Maryland School of Medicine, Baltimore, MD, USA.
| | | | - Mary Kay Lobo
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | | | | | - Linda Chang
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | - Dana Gabuzda
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Michelle Giglio
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | | | - Eran Hadas
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian R Herb
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Wen Hu
- Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | | | - Cheyu Lee
- University of California Irvine, Irvine, CA, USA
| | - Shuhui Liu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiaokun Liu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Anup A Mahurkar
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | - Meng Niu
- University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | | | - Piya Pillai
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - W Brad Ruzicka
- McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | | | | | | | - Allen Wang
- University of California San Diego, La Jolla, CA, USA
| | - Lauren Wills
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Siwei Xu
- University of California Irvine, Irvine, CA, USA
| | | | - Maryam Zand
- University of California San Diego, La Jolla, CA, USA
| | - Le Zhang
- Yale School of Medicine, New Haven, CT, USA
| | - Jing Zhang
- University of California Irvine, Irvine, CA, USA
| | | | - Shilpa Buch
- University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | - Howard S Fox
- University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | - Myriam Heiman
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ya-Chi Ho
- Yale School of Medicine, New Haven, CT, USA
| | - Manolis Kellis
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul J Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - David J Moore
- University of California San Diego, La Jolla, CA, USA
| | - Susan Morgello
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Tariq M Rana
- University of California San Diego, La Jolla, CA, USA
| | | | | | | | | | | | | | - David J Volsky
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Owen R White
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
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Tremblay C, Aslam S, Walker JE, Lorenzini I, Intorcia AJ, Arce RA, Choudhury P, Adler CH, Shill HA, Driver-Dunckley E, Mehta S, Piras IS, Belden CM, Atri A, Beach TG, Serrano GE. RNA sequencing of olfactory bulb in Parkinson's disease reveals gene alterations associated with olfactory dysfunction. Neurobiol Dis 2024; 196:106514. [PMID: 38663633 PMCID: PMC11132317 DOI: 10.1016/j.nbd.2024.106514] [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: 02/19/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 04/29/2024] Open
Abstract
The olfactory bulb is involved early in the pathophysiology of Parkinson's disease (PD), which is consistent with the early onset of olfactory dysfunction. Identifying the molecular mechanisms through which PD affects the olfactory bulb could lead to a better understanding of the pathophysiology and etiology of olfactory dysfunction in PD. We specifically aimed to assess gene expression changes, affected pathways and co-expression network by whole transcriptomic profiling of the olfactory bulb in subjects with clinicopathologically defined PD. Bulk RNA sequencing was performed on frozen human olfactory bulbs of 20 PD and 20 controls without dementia or any other neurodegenerative disorder, from the Arizona Study of Aging and Neurodegenerative disorders and the Brain and Body Donation Program. Differential expression analysis (19 PD vs 19 controls) revealed 2164 significantly differentially expressed genes (1090 upregulated and 1074 downregulated) in PD. Pathways enriched in downregulated genes included oxidative phosphorylation, olfactory transduction, metabolic pathways, and neurotransmitters synapses while immune and inflammatory responses as well as cellular death related pathways were enriched within upregulated genes. An overrepresentation of microglial and astrocyte-related genes was observed amongst upregulated genes, and excitatory neuron-related genes were overrepresented amongst downregulated genes. Co-expression network analysis revealed significant modules highly correlated with PD and olfactory dysfunction that were found to be involved in the MAPK signaling pathway, cytokine-cytokine receptor interaction, cholinergic synapse, and metabolic pathways. LAIR1 (leukocyte associated immunoglobulin like receptor 1) and PPARA (peroxisome proliferator activated receptor alpha) were identified as hub genes with a high discriminative power between PD and controls reinforcing an important role of neuroinflammation in the olfactory bulb of PD subjects. Olfactory identification test score positively correlated with expression of genes coding for G-coupled protein, glutamatergic, GABAergic, and cholinergic receptor proteins and negatively correlated with genes for proteins expressed in glial olfactory ensheathing cells. In conclusion, this study reveals gene alterations associated with neuroinflammation, neurotransmitter dysfunction, and disruptions of factors involved in the initiation of olfactory transduction signaling that may be involved in PD-related olfactory dysfunction.
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Affiliation(s)
| | - Sidra Aslam
- Banner Sun Health Research Institute, Sun City, AZ, USA
| | | | | | | | | | | | - Charles H Adler
- Department of Neurology, Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Holly A Shill
- Department of Neurology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Erika Driver-Dunckley
- Department of Neurology, Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Shyamal Mehta
- Department of Neurology, Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Alireza Atri
- Banner Sun Health Research Institute, Sun City, AZ, USA; Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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Wang HLV, Xiang JF, Yuan C, Veire AM, Gendron TF, Murray ME, Tansey MG, Hu J, Gearing M, Glass JD, Jin P, Corces VG, McEachin ZT. pTDP-43 levels correlate with cell type specific molecular alterations in the prefrontal cortex of C9orf72 ALS/FTD patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.12.523820. [PMID: 36711601 PMCID: PMC9882184 DOI: 10.1101/2023.01.12.523820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Repeat expansions in the C9orf72 gene are the most common genetic cause of amyotrophic lateral sclerosis and familial frontotemporal dementia (ALS/FTD). To identify molecular defects that take place in the dorsolateral frontal cortex of patients with C9orf72 ALS/FTD, we compared healthy controls with C9orf72 ALS/FTD donor samples staged based on the levels of cortical phosphorylated TAR DNA binding protein (pTDP-43), a neuropathological hallmark of disease progression. We identified distinct molecular changes in different cell types that take place during FTD development. Loss of neurosurveillance microglia and activation of the complement cascade take place early, when pTDP-43 aggregates are absent or very low, and become more pronounced in late stages, suggesting an initial involvement of microglia in disease progression. Reduction of layer 2-3 cortical projection neurons with high expression of CUX2/LAMP5 also occurs early, and the reduction becomes more pronounced as pTDP-43 accumulates. Several unique features were observed only in samples with high levels of pTDP-43, including global alteration of chromatin accessibility in oligodendrocytes, microglia, and astrocytes; higher ratios of premature oligodendrocytes; increased levels of the noncoding RNA NEAT1 in astrocytes and neurons, and higher amount of phosphorylated ribosomal protein S6. Our findings reveal previously unknown progressive functional changes in major cell types found in the frontal cortex of C9orf72 ALS/FTD patients that shed light on the mechanisms underlying the pathology of this disease.
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Affiliation(s)
- Hsiao-Lin V. Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Emory Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322
| | - Jian-Feng Xiang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Chenyang Yuan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Austin M. Veire
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224
| | | | | | - Malú G. Tansey
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32607
- Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32607
| | - Jian Hu
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Marla Gearing
- Emory Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322
| | - Jonathan D. Glass
- Emory Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Emory Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322
| | - Victor G. Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Emory Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322
| | - Zachary T. McEachin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Emory Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322
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