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Hudgins AD, Zhou S, Arey RN, Rosenfeld MG, Murphy CT, Suh Y. A systems biology-based identification and in vivo functional screening of Alzheimer's disease risk genes reveal modulators of memory function. Neuron 2024; 112:2112-2129.e4. [PMID: 38692279 PMCID: PMC11223975 DOI: 10.1016/j.neuron.2024.04.009] [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: 07/16/2022] [Revised: 10/18/2023] [Accepted: 04/08/2024] [Indexed: 05/03/2024]
Abstract
Genome-wide association studies (GWASs) have uncovered over 75 genomic loci associated with risk for late-onset Alzheimer's disease (LOAD), but identification of the underlying causal genes remains challenging. Studies of induced pluripotent stem cell (iPSC)-derived neurons from LOAD patients have demonstrated the existence of neuronal cell-intrinsic functional defects. Here, we searched for genetic contributions to neuronal dysfunction in LOAD using an integrative systems approach that incorporated multi-evidence-based gene mapping and network-analysis-based prioritization. A systematic perturbation screening of candidate risk genes in Caenorhabditis elegans (C. elegans) revealed that neuronal knockdown of the LOAD risk gene orthologs vha-10 (ATP6V1G2), cmd-1 (CALM3), amph-1 (BIN1), ephx-1 (NGEF), and pho-5 (ACP2) alters short-/intermediate-term memory function, the cognitive domain affected earliest during LOAD progression. These results highlight the impact of LOAD risk genes on evolutionarily conserved memory function, as mediated through neuronal endosomal dysfunction, and identify new targets for further mechanistic interrogation.
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Affiliation(s)
- Adam D Hudgins
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Shiyi Zhou
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Rachel N Arey
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael G Rosenfeld
- Department of Medicine, School of Medicine, University of California, La Jolla, CA, USA; Howard Hughes Medical Institute, University of California, La Jolla, CA, USA
| | - Coleen T Murphy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA; LSI Genomics, Princeton University, Princeton, NJ, USA.
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.
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2
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Trumpff C, Monzel AS, Sandi C, Menon V, Klein HU, Fujita M, Lee A, Petyuk VA, Hurst C, Duong DM, Seyfried NT, Wingo AP, Wingo TS, Wang Y, Thambisetty M, Ferrucci L, Bennett DA, De Jager PL, Picard M. Psychosocial experiences are associated with human brain mitochondrial biology. Proc Natl Acad Sci U S A 2024; 121:e2317673121. [PMID: 38889126 DOI: 10.1073/pnas.2317673121] [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: 10/11/2023] [Accepted: 04/30/2024] [Indexed: 06/20/2024] Open
Abstract
Psychosocial experiences affect brain health and aging trajectories, but the molecular pathways underlying these associations remain unclear. Normal brain function relies on energy transformation by mitochondria oxidative phosphorylation (OxPhos). Two main lines of evidence position mitochondria both as targets and drivers of psychosocial experiences. On the one hand, chronic stress exposure and mood states may alter multiple aspects of mitochondrial biology; on the other hand, functional variations in mitochondrial OxPhos capacity may alter social behavior, stress reactivity, and mood. But are psychosocial exposures and subjective experiences linked to mitochondrial biology in the human brain? By combining longitudinal antemortem assessments of psychosocial factors with postmortem brain (dorsolateral prefrontal cortex) proteomics in older adults, we find that higher well-being is linked to greater abundance of the mitochondrial OxPhos machinery, whereas higher negative mood is linked to lower OxPhos protein content. Combined, positive and negative psychosocial factors explained 18 to 25% of the variance in the abundance of OxPhos complex I, the primary biochemical entry point that energizes brain mitochondria. Moreover, interrogating mitochondrial psychobiological associations in specific neuronal and nonneuronal brain cells with single-nucleus RNA sequencing (RNA-seq) revealed strong cell-type-specific associations for positive psychosocial experiences and mitochondria in glia but opposite associations in neurons. As a result, these "mind-mitochondria" associations were masked in bulk RNA-seq, highlighting the likely underestimation of true psychobiological effect sizes in bulk brain tissues. Thus, self-reported psychosocial experiences are linked to human brain mitochondrial phenotypes.
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Affiliation(s)
- Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY 10032
| | - Anna S Monzel
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY 10032
| | - Carmen Sandi
- Laboratory of Behavioral Genetics, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Vilas Menon
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY 10032
| | - Hans-Ulrich Klein
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY 10032
| | - Masashi Fujita
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY 10032
| | - Annie Lee
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY 10032
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Cheyenne Hurst
- Department of Biochemistry, Emory University, Atlanta, GA 30329
| | - Duc M Duong
- Department of Biochemistry, Emory University, Atlanta, GA 30329
| | | | - Aliza P Wingo
- Department of Neurology and Human Genetics, School of Medicine, Emory University, Atlanta, GA 30329
| | - Thomas S Wingo
- Department of Neurology and Human Genetics, School of Medicine, Emory University, Atlanta, GA 30329
| | - Yanling Wang
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging Intramural Research Program, Baltimore, MD 21224
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892
| | - David A Bennett
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612
| | - Philip L De Jager
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY 10032
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY 10032
- Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY 10032
- Division of Behavioral Medicine, New York State Psychiatric Institute, New York, NY 10032
- Robert N. Butler Columbia Aging Center, Mailman School of Public Health, Columbia University, New York, NY 10032
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3
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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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4
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Irastorza-Valera L, Soria-Gómez E, Benitez JM, Montáns FJ, Saucedo-Mora L. Review of the Brain's Behaviour after Injury and Disease for Its Application in an Agent-Based Model (ABM). Biomimetics (Basel) 2024; 9:362. [PMID: 38921242 PMCID: PMC11202129 DOI: 10.3390/biomimetics9060362] [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: 05/06/2024] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
The brain is the most complex organ in the human body and, as such, its study entails great challenges (methodological, theoretical, etc.). Nonetheless, there is a remarkable amount of studies about the consequences of pathological conditions on its development and functioning. This bibliographic review aims to cover mostly findings related to changes in the physical distribution of neurons and their connections-the connectome-both structural and functional, as well as their modelling approaches. It does not intend to offer an extensive description of all conditions affecting the brain; rather, it presents the most common ones. Thus, here, we highlight the need for accurate brain modelling that can subsequently be used to understand brain function and be applied to diagnose, track, and simulate treatments for the most prevalent pathologies affecting the brain.
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Affiliation(s)
- Luis Irastorza-Valera
- E.T.S. de Ingeniería Aeronáutica y del Espacio, Universidad Politécnica de Madrid, Pza. Cardenal Cisneros 3, 28040 Madrid, Spain; (L.I.-V.); (J.M.B.); (F.J.M.)
- PIMM Laboratory, ENSAM–Arts et Métiers ParisTech, 151 Bd de l’Hôpital, 75013 Paris, France
| | - Edgar Soria-Gómez
- Achúcarro Basque Center for Neuroscience, Barrio Sarriena, s/n, 48940 Leioa, Spain;
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi, 5, 48009 Bilbao, Spain
- Department of Neurosciences, University of the Basque Country UPV/EHU, Barrio Sarriena, s/n, 48940 Leioa, Spain
| | - José María Benitez
- E.T.S. de Ingeniería Aeronáutica y del Espacio, Universidad Politécnica de Madrid, Pza. Cardenal Cisneros 3, 28040 Madrid, Spain; (L.I.-V.); (J.M.B.); (F.J.M.)
| | - Francisco J. Montáns
- E.T.S. de Ingeniería Aeronáutica y del Espacio, Universidad Politécnica de Madrid, Pza. Cardenal Cisneros 3, 28040 Madrid, Spain; (L.I.-V.); (J.M.B.); (F.J.M.)
- Department of Mechanical and Aerospace Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Luis Saucedo-Mora
- E.T.S. de Ingeniería Aeronáutica y del Espacio, Universidad Politécnica de Madrid, Pza. Cardenal Cisneros 3, 28040 Madrid, Spain; (L.I.-V.); (J.M.B.); (F.J.M.)
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology (MIT), 77 Massachusetts Ave, Cambridge, MA 02139, USA
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5
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Chien JF, Liu H, Wang BA, Luo C, Bartlett A, Castanon R, Johnson ND, Nery JR, Osteen J, Li J, Altshul J, Kenworthy M, Valadon C, Liem M, Claffey N, O'Connor C, Seeker LA, Ecker JR, Behrens MM, Mukamel EA. Cell-type-specific effects of age and sex on human cortical neurons. Neuron 2024:S0896-6273(24)00360-X. [PMID: 38838671 DOI: 10.1016/j.neuron.2024.05.013] [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: 11/29/2023] [Revised: 03/29/2024] [Accepted: 05/09/2024] [Indexed: 06/07/2024]
Abstract
Altered transcriptional and epigenetic regulation of brain cell types may contribute to cognitive changes with advanced age. Using single-nucleus multi-omic DNA methylation and transcriptome sequencing (snmCT-seq) in frontal cortex from young adult and aged donors, we found widespread age- and sex-related variation in specific neuron types. The proportion of inhibitory SST- and VIP-expressing neurons was reduced in aged donors. Excitatory neurons had more profound age-related changes in their gene expression and DNA methylation than inhibitory cells. Hundreds of genes involved in synaptic activity, including EGR1, were less expressed in aged adults. Genes located in subtelomeric regions increased their expression with age and correlated with reduced telomere length. We further mapped cell-type-specific sex differences in gene expression and X-inactivation escape genes. Multi-omic single-nucleus epigenomes and transcriptomes provide new insight into the effects of age and sex on human neurons.
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Affiliation(s)
- Jo-Fan Chien
- Department of Physics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Bang-An Wang
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Rosa Castanon
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Nicholas D Johnson
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92037, USA; Computational Neurobiology Laboratory, Salk Institute, La Jolla, CA 92037, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Julia Osteen
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Junhao Li
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jordan Altshul
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Mia Kenworthy
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Cynthia Valadon
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Michelle Liem
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Naomi Claffey
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Carolyn O'Connor
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Luise A Seeker
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA.
| | - M Margarita Behrens
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92037, USA; Computational Neurobiology Laboratory, Salk Institute, La Jolla, CA 92037, USA.
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA.
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6
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Lee AT, Chang EF, Paredes MF, Nowakowski TJ. Large-scale neurophysiology and single-cell profiling in human neuroscience. Nature 2024; 630:587-595. [PMID: 38898291 DOI: 10.1038/s41586-024-07405-0] [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: 07/06/2023] [Accepted: 04/09/2024] [Indexed: 06/21/2024]
Abstract
Advances in large-scale single-unit human neurophysiology, single-cell RNA sequencing, spatial transcriptomics and long-term ex vivo tissue culture of surgically resected human brain tissue have provided an unprecedented opportunity to study human neuroscience. In this Perspective, we describe the development of these paradigms, including Neuropixels and recent brain-cell atlas efforts, and discuss how their convergence will further investigations into the cellular underpinnings of network-level activity in the human brain. Specifically, we introduce a workflow in which functionally mapped samples of human brain tissue resected during awake brain surgery can be cultured ex vivo for multi-modal cellular and functional profiling. We then explore how advances in human neuroscience will affect clinical practice, and conclude by discussing societal and ethical implications to consider. Potential findings from the field of human neuroscience will be vast, ranging from insights into human neurodiversity and evolution to providing cell-type-specific access to study and manipulate diseased circuits in pathology. This Perspective aims to provide a unifying framework for the field of human neuroscience as we welcome an exciting era for understanding the functional cytoarchitecture of the human brain.
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Affiliation(s)
- Anthony T Lee
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Edward F Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mercedes F Paredes
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA.
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
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7
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Wu Y, Libby JB, Dumitrescu L, De Jager PL, Menon V, Schneider JA, Bennett DA, Hohman TJ. Association of 10 VEGF Family Genes with Alzheimer's Disease Endophenotypes at Single Cell Resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589221. [PMID: 38826287 PMCID: PMC11142115 DOI: 10.1101/2024.04.12.589221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The cell-type specific role of the vascular endothelial growth factors (VEGFs) in the pathogenesis of Alzheimer's disease (AD) is not well characterized. In this study, we utilized a single-nucleus RNA sequencing dataset from Dorsolateral Prefrontal Cortex (DLFPC) of 424 donors from the Religious Orders Study and Memory and Aging Project (ROS/MAP) to investigate the effect of 10 VEGF genes ( VEGFA, VEGFB, VEGFC, VEGFD, PGF, FLT1, FLT4, KDR, NRP1 , and NRP2 ) on AD endophenotypes. Mean age of death was 89 years, among which 68% were females, and 52% has AD dementia. Negative binomial mixed models were used for differential expression analysis and for association analysis with β-amyloid load, PHF tau tangle density, and both cross-sectional and longitudinal global cognitive function. Intercellular VEGF-associated signaling was profiled using CellChat. We discovered prefrontal cortical FLT1 expression was upregulated in AD brains in both endothelial and microglial cells. Higher FLT1 expression was also associated with worse cross-sectional global cognitive function, longitudinal cognitive trajectories, and β-amyloid load. Similarly, higher endothelial FLT4 expression was associated with more β-amyloid load. In contrast to the receptors, VEGFB showed opposing effects on β-amyloid load whereby higher levels in oligodendrocytes was associated with high amyloid burden, while higher levels in inhibitory neurons was associated with lower amyloid burden. Finally, AD cells showed significant reduction in overall VEGF signaling comparing to those from cognitive normal participants. Our results highlight key changes in VEGF receptor expression in endothelial and microglial cells during AD, and the potential protective role of VEGFB in neurons.
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8
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Gouveia Roque C, Phatnani H, Hengst U. The broken Alzheimer's disease genome. CELL GENOMICS 2024; 4:100555. [PMID: 38697121 PMCID: PMC11099344 DOI: 10.1016/j.xgen.2024.100555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/25/2024] [Accepted: 04/07/2024] [Indexed: 05/04/2024]
Abstract
The complex pathobiology of late-onset Alzheimer's disease (AD) poses significant challenges to therapeutic and preventative interventions. Despite these difficulties, genomics and related disciplines are allowing fundamental mechanistic insights to emerge with clarity, particularly with the introduction of high-resolution sequencing technologies. After all, the disrupted processes at the interface between DNA and gene expression, which we call the broken AD genome, offer detailed quantitative evidence unrestrained by preconceived notions about the disease. In addition to highlighting biological pathways beyond the classical pathology hallmarks, these advances have revitalized drug discovery efforts and are driving improvements in clinical tools. We review genetic, epigenomic, and gene expression findings related to AD pathogenesis and explore how their integration enables a better understanding of the multicellular imbalances contributing to this heterogeneous condition. The frontiers opening on the back of these research milestones promise a future of AD care that is both more personalized and predictive.
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Affiliation(s)
- Cláudio Gouveia Roque
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA; Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University, New York, NY 10032, USA
| | - Ulrich Hengst
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Pathology & Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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9
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Kampmann M. Molecular and cellular mechanisms of selective vulnerability in neurodegenerative diseases. Nat Rev Neurosci 2024; 25:351-371. [PMID: 38575768 DOI: 10.1038/s41583-024-00806-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2024] [Indexed: 04/06/2024]
Abstract
The selective vulnerability of specific neuronal subtypes is a hallmark of neurodegenerative diseases. In this Review, I summarize our current understanding of the brain regions and cell types that are selectively vulnerable in different neurodegenerative diseases and describe the proposed underlying cell-autonomous and non-cell-autonomous mechanisms. I highlight how recent methodological innovations - including single-cell transcriptomics, CRISPR-based screens and human cell-based models of disease - are enabling new breakthroughs in our understanding of selective vulnerability. An understanding of the molecular mechanisms that determine selective vulnerability and resilience would shed light on the key processes that drive neurodegeneration and point to potential therapeutic strategies to protect vulnerable cell populations.
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Affiliation(s)
- Martin Kampmann
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.
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10
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Gaur P, Bryois J, Calini D, Foo L, Hoozemans JJM, Malhotra D, Menon V. Single-nucleus and spatial transcriptomic profiling of human temporal cortex and white matter reveals novel associations with AD pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590816. [PMID: 38712204 PMCID: PMC11071354 DOI: 10.1101/2024.04.23.590816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder with complex pathological manifestations and is the leading cause of cognitive decline and dementia in elderly individuals. A major goal in AD research is to identify new therapeutic pathways by studying the molecular and cellular changes in the disease, either downstream or upstream of the pathological hallmarks. In this study, we present a comprehensive investigation of cellular heterogeneity from the temporal cortex region of 40 individuals, comprising healthy donors and individuals with differing tau and amyloid burden. Using single-nucleus transcriptome analysis of 430,271 nuclei from both gray and white matter of these individuals, we identified cell type-specific subclusters in both neuronal and glial cell types with varying degrees of association with AD pathology. In particular, these associations are present in layer specific glutamatergic (excitatory) neuronal types, along with GABAergic (inhibitory) neurons and glial subtypes. These associations were observed in early as well as late pathological progression. We extended this analysis by performing multiplexed in situ hybridization using the CARTANA platform, capturing 155 genes in 13 individuals with varying levels of tau pathology. By modeling the spatial distribution of these genes and their associations with the pathology, we not only replicated key findings from our snRNA data analysis, but also identified a set of cell type-specific genes that show selective enrichment or depletion near pathological inclusions. Together, our findings allow us to prioritize specific cell types and pathways for targeted interventions at various stages of pathological progression in AD.
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Affiliation(s)
- Pallavi Gaur
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, NY, USA
| | - Julien Bryois
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Daniela Calini
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Lynette Foo
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Jeroen J M Hoozemans
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Dheeraj Malhotra
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
- MS Research Unit, Biogen, Cambridge, MA, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, NY, USA
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11
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de Vries LE, Jongejan A, Monteiro Fortes J, Balesar R, Rozemuller AJM, Moerland PD, Huitinga I, Swaab DF, Verhaagen J. Gene-expression profiling of individuals resilient to Alzheimer's disease reveals higher expression of genes related to metallothionein and mitochondrial processes and no changes in the unfolded protein response. Acta Neuropathol Commun 2024; 12:68. [PMID: 38664739 PMCID: PMC11046840 DOI: 10.1186/s40478-024-01760-9] [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: 01/10/2024] [Accepted: 03/10/2024] [Indexed: 04/28/2024] Open
Abstract
Some individuals show a discrepancy between cognition and the amount of neuropathological changes characteristic for Alzheimer's disease (AD). This phenomenon has been referred to as 'resilience'. The molecular and cellular underpinnings of resilience remain poorly understood. To obtain an unbiased understanding of the molecular changes underlying resilience, we investigated global changes in gene expression in the superior frontal gyrus of a cohort of cognitively and pathologically well-defined AD patients, resilient individuals and age-matched controls (n = 11-12 per group). 897 genes were significantly altered between AD and control, 1121 between resilient and control and 6 between resilient and AD. Gene set enrichment analysis (GSEA) revealed that the expression of metallothionein (MT) and of genes related to mitochondrial processes was higher in the resilient donors. Weighted gene co-expression network analysis (WGCNA) identified gene modules related to the unfolded protein response, mitochondrial processes and synaptic signaling to be differentially associated with resilience or dementia. As changes in MT, mitochondria, heat shock proteins and the unfolded protein response (UPR) were the most pronounced changes in the GSEA and/or WGCNA, immunohistochemistry was used to further validate these processes. MT was significantly increased in astrocytes in resilient individuals. A higher proportion of the mitochondrial gene MT-CO1 was detected outside the cell body versus inside the cell body in the resilient compared to the control group and there were higher levels of heat shock protein 70 (HSP70) and X-box-binding protein 1 spliced (XBP1s), two proteins related to heat shock proteins and the UPR, in the AD donors. Finally, we show evidence for putative sex-specific alterations in resilience, including gene expression differences related to autophagy in females compared to males. Taken together, these results show possible mechanisms involving MTs, mitochondrial processes and the UPR by which individuals might maintain cognition despite the presence of AD pathology.
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Affiliation(s)
- Luuk E de Vries
- Department of Neuroregeneration, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands.
| | - Aldo Jongejan
- Amsterdam UMC Location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Jennifer Monteiro Fortes
- Department of Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands
| | - Rawien Balesar
- Department of Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands
| | - Annemieke J M Rozemuller
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC - Location VUmc, Amsterdam, The Netherlands
| | - Perry D Moerland
- Amsterdam UMC Location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Inge Huitinga
- Department of Neuroimmunology, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Dick F Swaab
- Department of Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands
| | - Joost Verhaagen
- Department of Neuroregeneration, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands.
- Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
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12
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Haq I, Ngo JC, Roy N, Pan RL, Nawsheen N, Chiu R, Zhang Y, Fujita M, Soni RK, Wu X, Bennett DA, Menon V, Olah M, Sher F. An integrated toolkit for human microglia functional genomics. Stem Cell Res Ther 2024; 15:104. [PMID: 38600587 PMCID: PMC11005142 DOI: 10.1186/s13287-024-03700-9] [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: 09/28/2023] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Microglia, the brain's resident immune cells, play vital roles in brain development, and disorders like Alzheimer's disease (AD). Human iPSC-derived microglia (iMG) provide a promising model to study these processes. However, existing iMG generation protocols face challenges, such as prolonged differentiation time, lack of detailed characterization, and limited gene function investigation via CRISPR-Cas9. METHODS Our integrated toolkit for in-vitro microglia functional genomics optimizes iPSC differentiation into iMG through a streamlined two-step, 20-day process, producing iMG with a normal karyotype. We confirmed the iMG's authenticity and quality through single-cell RNA sequencing, chromatin accessibility profiles (ATAC-Seq), proteomics and functional tests. The toolkit also incorporates a drug-dependent CRISPR-ON/OFF system for temporally controlled gene expression. Further, we facilitate the use of multi-omic data by providing online searchable platform that compares new iMG profiles to human primary microglia: https://sherlab.shinyapps.io/IPSC-derived-Microglia/ . RESULTS Our method generates iMG that closely align with human primary microglia in terms of transcriptomic, proteomic, and chromatin accessibility profiles. Functionally, these iMG exhibit Ca2 + transients, cytokine driven migration, immune responses to inflammatory signals, and active phagocytosis of CNS related substrates including synaptosomes, amyloid beta and myelin. Significantly, the toolkit facilitates repeated iMG harvesting, essential for large-scale experiments like CRISPR-Cas9 screens. The standalone ATAC-Seq profiles of our iMG closely resemble primary microglia, positioning them as ideal tools to study AD-associated single nucleotide variants (SNV) especially in the genome regulatory regions. CONCLUSIONS Our advanced two-step protocol rapidly and efficiently produces authentic iMG. With features like the CRISPR-ON/OFF system and a comprehensive multi-omic data platform, our toolkit equips researchers for robust microglial functional genomic studies. By facilitating detailed SNV investigation and offering a sustainable cell harvest mechanism, the toolkit heralds significant progress in neurodegenerative disease drug research and therapeutic advancement.
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Affiliation(s)
- Imdadul Haq
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Jason C Ngo
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Nainika Roy
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Richard L Pan
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Nadiya Nawsheen
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Rebecca Chiu
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Neuroimmunology Core, Center for Translational & Computational Neuroimmunology, Division of Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Ya Zhang
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Neuroimmunology Core, Center for Translational & Computational Neuroimmunology, Division of Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Masashi Fujita
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Rajesh K Soni
- Proteomics Core, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Xuebing Wu
- Department of Medicine, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Marta Olah
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Falak Sher
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA.
- Department of Neurology, Columbia University Medical Center, New York, NY, USA.
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13
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de Vries LE, Huitinga I, Kessels HW, Swaab DF, Verhaagen J. The concept of resilience to Alzheimer's Disease: current definitions and cellular and molecular mechanisms. Mol Neurodegener 2024; 19:33. [PMID: 38589893 PMCID: PMC11003087 DOI: 10.1186/s13024-024-00719-7] [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: 08/23/2023] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
Some individuals are able to maintain their cognitive abilities despite the presence of significant Alzheimer's Disease (AD) neuropathological changes. This discrepancy between cognition and pathology has been labeled as resilience and has evolved into a widely debated concept. External factors such as cognitive stimulation are associated with resilience to AD, but the exact cellular and molecular underpinnings are not completely understood. In this review, we discuss the current definitions used in the field, highlight the translational approaches used to investigate resilience to AD and summarize the underlying cellular and molecular substrates of resilience that have been derived from human and animal studies, which have received more and more attention in the last few years. From these studies the picture emerges that resilient individuals are different from AD patients in terms of specific pathological species and their cellular reaction to AD pathology, which possibly helps to maintain cognition up to a certain tipping point. Studying these rare resilient individuals can be of great importance as it could pave the way to novel therapeutic avenues for AD.
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Affiliation(s)
- Luuk E de Vries
- Department of Neuroregeneration, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands.
| | - Inge Huitinga
- Department of Neuroimmunology, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
| | - Helmut W Kessels
- Swammerdam Institute for Life Sciences, Amsterdam Neuroscience, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
| | - Dick F Swaab
- Department of Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, Netherlands
| | - Joost Verhaagen
- Department of Neuroregeneration, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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14
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Fiorini MR, Dilliott AA, Thomas RA, Farhan SMK. Transcriptomics of Human Brain Tissue in Parkinson's Disease: a Comparison of Bulk and Single-cell RNA Sequencing. Mol Neurobiol 2024:10.1007/s12035-024-04124-5. [PMID: 38578357 DOI: 10.1007/s12035-024-04124-5] [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: 10/11/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024]
Abstract
Parkinson's disease (PD) is a chronic and progressive neurodegenerative disease leading to motor dysfunction and, in some cases, dementia. Transcriptome analysis is one promising approach for characterizing PD and other neurodegenerative disorders by informing how specific disease events influence gene expression and contribute to pathogenesis. With the emergence of single-cell and single-nucleus RNA sequencing (scnRNA-seq) technologies, the transcriptional landscape of neurodegenerative diseases can now be described at the cellular level. As the application of scnRNA-seq is becoming routine, it calls to question how results at a single-cell resolution compare to those obtained from RNA sequencing of whole tissues (bulk RNA-seq), whether the findings are compatible, and how the assays are complimentary for unraveling the elusive transcriptional changes that drive neurodegenerative disease. Herein, we review the studies that have leveraged RNA-seq technologies to investigate PD. Through the integration of bulk and scnRNA-seq findings from human, post-mortem brain tissue, we use the PD literature as a case study to evaluate the compatibility of the results generated from each assay and demonstrate the complementarity of the sequencing technologies. Finally, through the lens of the PD transcriptomic literature, we evaluate the current feasibility of bulk and scnRNA-seq technologies to illustrate the necessity of both technologies for achieving a comprehensive insight into the mechanism by which gene expression promotes neurodegenerative disease. We conclude that the continued application of both assays will provide the greatest insight into neurodegenerative disease pathology, providing both cell-specific and whole-tissue level information.
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Affiliation(s)
- Michael R Fiorini
- The Montreal Neurological Institute-Hospital, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Allison A Dilliott
- The Montreal Neurological Institute-Hospital, Montreal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Rhalena A Thomas
- The Montreal Neurological Institute-Hospital, Montreal, QC, Canada.
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.
| | - Sali M K Farhan
- The Montreal Neurological Institute-Hospital, Montreal, QC, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.
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15
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Fujita M, Gao Z, Zeng L, McCabe C, White CC, Ng B, Green GS, Rozenblatt-Rosen O, Phillips D, Amir-Zilberstein L, Lee H, Pearse RV, Khan A, Vardarajan BN, Kiryluk K, Ye CJ, Klein HU, Wang G, Regev A, Habib N, Schneider JA, Wang Y, Young-Pearse T, Mostafavi S, Bennett DA, Menon V, De Jager PL. Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain. Nat Genet 2024; 56:605-614. [PMID: 38514782 DOI: 10.1038/s41588-024-01685-y] [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: 12/16/2022] [Accepted: 02/08/2024] [Indexed: 03/23/2024]
Abstract
The relationship between genetic variation and gene expression in brain cell types and subtypes remains understudied. Here, we generated single-nucleus RNA sequencing data from the neocortex of 424 individuals of advanced age; we assessed the effect of genetic variants on RNA expression in cis (cis-expression quantitative trait loci) for seven cell types and 64 cell subtypes using 1.5 million transcriptomes. This effort identified 10,004 eGenes at the cell type level and 8,099 eGenes at the cell subtype level. Many eGenes are only detected within cell subtypes. A new variant influences APOE expression only in microglia and is associated with greater cerebral amyloid angiopathy but not Alzheimer's disease pathology, after adjusting for APOEε4, providing mechanistic insights into both pathologies. Furthermore, only a TMEM106B variant affects the proportion of cell subtypes. Integration of these results with genome-wide association studies highlighted the targeted cell type and probable causal gene within Alzheimer's disease, schizophrenia, educational attainment and Parkinson's disease loci.
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Affiliation(s)
- Masashi Fujita
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Zongmei Gao
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lu Zeng
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charles C White
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Bernard Ng
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Gilad Sahar Green
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Devan Phillips
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | | | - Hyo Lee
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Atlas Khan
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Badri N Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY, USA
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Hans-Ulrich Klein
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Gao Wang
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Naomi Habib
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Tracy Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sara Mostafavi
- Department of Statistics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.
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16
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Butler ML, Pervaiz N, Ypsilantis P, Wang Y, Cammasola Breda J, Mazzilli S, Nicks R, Spurlock E, Hefti MM, Huber BR, Alvarez VE, Stein TD, Campbell JD, McKee AC, Cherry JD. Repetitive head impacts induce neuronal loss and neuroinflammation in young athletes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586815. [PMID: 38585925 PMCID: PMC10996668 DOI: 10.1101/2024.03.26.586815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Repetitive head impacts (RHI) sustained from contact sports are the largest risk factor for chronic traumatic encephalopathy (CTE). Currently, CTE can only be diagnosed after death and the multicellular cascade of events that trigger initial hyperphosphorylated tau (p-tau) deposition remain unclear. Further, the symptoms endorsed by young individuals with early disease are not fully explained by the extent of p-tau deposition, severely hampering development of therapeutic interventions. Here, we show that RHI exposure associates with a multicellular response in young individuals (<51 years old) prior to the onset of CTE p-tau pathology that correlates with number of years of RHI exposure. Leveraging single nucleus RNA sequencing of tissue from 8 control, 9 RHI-exposed, and 11 low stage CTE individuals, we identify SPP1+ inflammatory microglia, angiogenic and inflamed endothelial cell profiles, reactive astrocytes, and altered synaptic gene expression in excitatory and inhibitory neurons in all individuals with exposure to RHI. Surprisingly, we also observe a significant loss of cortical sulcus layer 2/3 neurons in contact sport athletes compared to controls independent of p-tau pathology. These results provide robust evidence that multiple years of RHI exposure is sufficient to induce lasting cellular alterations that may underlie p-tau deposition and help explain the early clinical symptoms observed in young former contact sport athletes. Furthermore, these data identify specific cellular responses to repetitive head impacts that may direct future identification of diagnostic and therapeutic strategies for CTE.
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Affiliation(s)
- Morgane L.M.D. Butler
- Department of Anatomy & Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
- Boston University Alzheimer’s Disease and CTE Centers, Boston University Chobanian & Avedisian School of Medicine, Boston MA
| | - Nida Pervaiz
- Section of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | | | - Yichen Wang
- Section of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Julia Cammasola Breda
- Section of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Sarah Mazzilli
- Section of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | | | | | - Marco M. Hefti
- Department of Pathology, University of Iowa Health Care, Iowa City IA, USA
| | - Bertrand R. Huber
- VA Boston Healthcare System, Jamaica Plain MA, USA
- National Center for PTSD, VA Boston Healthcare System, Boston MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Victor E. Alvarez
- VA Boston Healthcare System, Jamaica Plain MA, USA
- VA Bedford Healthcare System, Bedford MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Thor D. Stein
- Boston University Alzheimer’s Disease and CTE Centers, Boston University Chobanian & Avedisian School of Medicine, Boston MA
- VA Boston Healthcare System, Jamaica Plain MA, USA
- VA Bedford Healthcare System, Bedford MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Joshua D. Campbell
- Section of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Ann C. McKee
- Boston University Alzheimer’s Disease and CTE Centers, Boston University Chobanian & Avedisian School of Medicine, Boston MA
- VA Boston Healthcare System, Jamaica Plain MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Jonathan D. Cherry
- Department of Anatomy & Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
- Boston University Alzheimer’s Disease and CTE Centers, Boston University Chobanian & Avedisian School of Medicine, Boston MA
- VA Boston Healthcare System, Jamaica Plain MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
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17
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Rybnicek J, Chen Y, Milic M, Tio ES, McLaurin J, Hohman TJ, De Jager PL, Schneider JA, Wang Y, Bennett DA, Tripathy S, Felsky D, Lambe EK. CHRNA5 links chandelier cells to severity of amyloid pathology in aging and Alzheimer's disease. Transl Psychiatry 2024; 14:83. [PMID: 38331937 PMCID: PMC10853183 DOI: 10.1038/s41398-024-02785-3] [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: 11/22/2022] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
Changes in high-affinity nicotinic acetylcholine receptors are intricately connected to neuropathology in Alzheimer's Disease (AD). Protective and cognitive-enhancing roles for the nicotinic α5 subunit have been identified, but this gene has not been closely examined in the context of human aging and dementia. Therefore, we investigate the nicotinic α5 gene CHRNA5 and the impact of relevant single nucleotide polymorphisms (SNPs) in prefrontal cortex from 922 individuals with matched genotypic and post-mortem RNA sequencing in the Religious Orders Study and Memory and Aging Project (ROS/MAP). We find that a genotype robustly linked to increased expression of CHRNA5 (rs1979905A2) predicts significantly reduced cortical β-amyloid load. Intriguingly, co-expression analysis suggests CHRNA5 has a distinct cellular expression profile compared to other nicotinic receptor genes. Consistent with this prediction, single nucleus RNA sequencing from 22 individuals reveals CHRNA5 expression is disproportionately elevated in chandelier neurons, a distinct subtype of inhibitory neuron known for its role in excitatory/inhibitory (E/I) balance. We show that chandelier neurons are enriched in amyloid-binding proteins compared to basket cells, the other major subtype of PVALB-positive interneurons. Consistent with the hypothesis that nicotinic receptors in chandelier cells normally protect against β-amyloid, cell-type proportion analysis from 549 individuals reveals these neurons show amyloid-associated vulnerability only in individuals with impaired function/trafficking of nicotinic α5-containing receptors due to homozygosity of the missense CHRNA5 SNP (rs16969968A2). Taken together, these findings suggest that CHRNA5 and its nicotinic α5 subunit exert a neuroprotective role in aging and Alzheimer's disease centered on chandelier interneurons.
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Affiliation(s)
- Jonas Rybnicek
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Yuxiao Chen
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Milos Milic
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Earvin S Tio
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - JoAnne McLaurin
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Timothy J Hohman
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Julie A Schneider
- Department of Pathology, Rush University, Chicago, IL, USA
- Department of Neurological Sciences, Rush University, Chicago, IL, USA
| | - Yanling Wang
- Department of Neurological Sciences, Rush University, Chicago, IL, USA
| | - David A Bennett
- Department of Neurological Sciences, Rush University, Chicago, IL, USA
| | - Shreejoy Tripathy
- Department of Physiology, University of Toronto, Toronto, ON, Canada.
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
| | - Evelyn K Lambe
- Department of Physiology, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
- Department of OBGYN, University of Toronto, Toronto, ON, Canada.
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18
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Joodaki M, Shaigan M, Parra V, Bülow RD, Kuppe C, Hölscher DL, Cheng M, Nagai JS, Goedertier M, Bouteldja N, Tesar V, Barratt J, Roberts IS, Coppo R, Kramann R, Boor P, Costa IG. Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT). Mol Syst Biol 2024; 20:57-74. [PMID: 38177382 PMCID: PMC10883279 DOI: 10.1038/s44320-023-00003-8] [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: 08/24/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 01/06/2024] Open
Abstract
Although clinical applications represent the next challenge in single-cell genomics and digital pathology, we still lack computational methods to analyze single-cell or pathomics data to find sample-level trajectories or clusters associated with diseases. This remains challenging as single-cell/pathomics data are multi-scale, i.e., a sample is represented by clusters of cells/structures, and samples cannot be easily compared with each other. Here we propose PatIent Level analysis with Optimal Transport (PILOT). PILOT uses optimal transport to compute the Wasserstein distance between two individual single-cell samples. This allows us to perform unsupervised analysis at the sample level and uncover trajectories or cellular clusters associated with disease progression. We evaluate PILOT and competing approaches in single-cell genomics or pathomics studies involving various human diseases with up to 600 samples/patients and millions of cells or tissue structures. Our results demonstrate that PILOT detects disease-associated samples from large and complex single-cell or pathomics data. Moreover, PILOT provides a statistical approach to find changes in cell populations, gene expression, and tissue structures related to the trajectories or clusters supporting interpretation of predictions.
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Affiliation(s)
- Mehdi Joodaki
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany
| | - Mina Shaigan
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany
| | - Victor Parra
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany
| | - Roman D Bülow
- Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - David L Hölscher
- Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Mingbo Cheng
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany
| | - James S Nagai
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany
| | - Michaël Goedertier
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany
- Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Nassim Bouteldja
- Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Vladimir Tesar
- Department of Nephrology, 1st Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | - Jonathan Barratt
- John Walls Renal Unit, University Hospital of Leicester National Health Service Trust, Leicester, UK
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Ian Sd Roberts
- Department of Cellular Pathology, Oxford University Hospitals National Health Services Foundation Trust, Oxford, UK
| | - Rosanna Coppo
- Fondazione Ricerca Molinette, Regina Margherita Children's University Hospital, Torino, Italy
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, Netherlands
| | - Peter Boor
- Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany.
| | - Ivan G Costa
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany.
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19
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Millet A, Ledo JH, Tavazoie SF. An exhausted-like microglial population accumulates in aged and APOE4 genotype Alzheimer's brains. Immunity 2024; 57:153-170.e6. [PMID: 38159571 PMCID: PMC10805152 DOI: 10.1016/j.immuni.2023.12.001] [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: 02/23/2023] [Revised: 10/04/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
The dominant risk factors for late-onset Alzheimer's disease (AD) are advanced age and the APOE4 genetic variant. To examine how these factors alter neuroimmune function, we generated an integrative, longitudinal single-cell atlas of brain immune cells in AD model mice bearing the three common human APOE alleles. Transcriptomic and chromatin accessibility analyses identified a reactive microglial population defined by the concomitant expression of inflammatory signals and cell-intrinsic stress markers whose frequency increased with age and APOE4 burden. An analogous population was detectable in the brains of human AD patients, including in the cortical tissue, using multiplexed spatial transcriptomics. This population, which we designate as terminally inflammatory microglia (TIM), exhibited defects in amyloid-β clearance and altered cell-cell communication during aducanumab treatment. TIM may represent an exhausted-like state for inflammatory microglia in the AD milieu that contributes to AD risk and pathology in APOE4 carriers and the elderly, thus presenting a potential therapeutic target for AD.
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Affiliation(s)
- Alon Millet
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA; Tri-Institutional Program in Computational Biology and Medicine, The Rockefeller University, New York, NY 10065, USA
| | - Jose Henrique Ledo
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA; Department of Pathology and Laboratory of Medicine, Department of Neuroscience, South Carolina Alzheimer's Disease Research Center, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA; Tri-Institutional Program in Computational Biology and Medicine, The Rockefeller University, New York, NY 10065, USA.
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20
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Lam M, Lee D, Kosater I, Khairallah A, Taga M, Zhang Y, Fujita M, Nag S, Bennett DA, De Jager P, Menon V. Human disease-specific cell signatures in non-lesional tissue in Multiple Sclerosis detected by single-cell and spatial transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572491. [PMID: 38187779 PMCID: PMC10769298 DOI: 10.1101/2023.12.20.572491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Recent investigations of cell type changes in Multiple Sclerosis (MS) using single-cell profiling methods have focused on active lesional and peri-lesional brain tissue, and have implicated a number of peripheral and central nervous system cell types. However, an important question is the extent to which so-called "normal-appearing" non-lesional tissue in individuals with MS accumulate changes over the lifespan. Here, we compared post-mortem non-lesional brain tissue from donors with a pathological or clinical diagnosis of MS from the Religious Orders Study or Rush Memory and Aging Project (ROSMAP) cohorts to age- and sex-matched brains from persons without MS (controls). We profiled three brain regions using single-nucleus RNA-seq: dorsolateral prefrontal cortex (DLPFC), normal appearing white matter (NAWM) and the pulvinar in thalamus (PULV), from 15 control individuals, 8 individuals with MS, and 5 individuals with other detrimental pathologies accompanied by demyelination, resulting in a total of 78 samples. We identified region- and cell type-specific differences in non-lesional samples from individuals diagnosed with MS and/or exhibiting secondary demyelination with other neurological conditions, as compared to control donors. These differences included lower proportions of oligodendrocytes with expression of myelination related genes MOBP, MBP, PLP1, as well as higher proportions of CRYAB+ oligodendrocytes in all three brain regions. Among microglial signatures, we identified subgroups that were higher in both demyelination (TMEM163+/ERC2+), as well as those that were specifically higher in MS donors (HIF1A+/SPP1+) and specifically in donors with secondary demyelination (SOCS6+/MYO1E+), in both white and grey matter. To validate our findings, we generated Visium spatial transcriptomics data on matched tissue from 13 donors, and recapitulated our observations of gene expression differences in oligodendrocytes and microglia. Finally, we show that some of the differences observed between control and MS donors in NAWM mirror those previously reported between control WM and active lesions in MS donors. Overall, our investigation sheds additional light on cell type- and disease-specific differences present even in non-lesional white and grey matter tissue, highlighting widespread cellular signatures that may be associated with downstream pathological changes.
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Affiliation(s)
- Matti Lam
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Dylan Lee
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Ivy Kosater
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Anthony Khairallah
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Mariko Taga
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Ya Zhang
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Masashi Fujita
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Sukriti Nag
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL
| | - Philip De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
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21
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Yang HS, Teng L, Kang D, Menon V, Ge T, Finucane HK, Schultz AP, Properzi M, Klein HU, Chibnik LB, Schneider JA, Bennett DA, Hohman TJ, Mayeux RP, Johnson KA, De Jager PL, Sperling RA. Cell-type-specific Alzheimer's disease polygenic risk scores are associated with distinct disease processes in Alzheimer's disease. Nat Commun 2023; 14:7659. [PMID: 38036535 PMCID: PMC10689816 DOI: 10.1038/s41467-023-43132-2] [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: 05/22/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Many of the Alzheimer's disease (AD) risk genes are specifically expressed in microglia and astrocytes, but how and when the genetic risk localizing to these cell types contributes to AD pathophysiology remains unclear. Here, we derive cell-type-specific AD polygenic risk scores (ADPRS) from two extensively characterized datasets and uncover the impact of cell-type-specific genetic risk on AD endophenotypes. In an autopsy dataset spanning all stages of AD (n = 1457), the astrocytic ADPRS affected diffuse and neuritic plaques (amyloid-β), while microglial ADPRS affected neuritic plaques, microglial activation, neurofibrillary tangles (tau), and cognitive decline. In an independent neuroimaging dataset of cognitively unimpaired elderly (n = 2921), astrocytic ADPRS was associated with amyloid-β, and microglial ADPRS was associated with amyloid-β and tau, connecting cell-type-specific genetic risk with AD pathology even before symptom onset. Together, our study provides human genetic evidence implicating multiple glial cell types in AD pathophysiology, starting from the preclinical stage.
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Affiliation(s)
- Hyun-Sik Yang
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Ling Teng
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel Kang
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Vilas Menon
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Tian Ge
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Hilary K Finucane
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Aaron P Schultz
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Michael Properzi
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Lori B Chibnik
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Timothy J Hohman
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Richard P Mayeux
- Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Keith A Johnson
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Reisa A Sperling
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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22
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Chou V, Pearse RV, Aylward AJ, Ashour N, Taga M, Terzioglu G, Fujita M, Fancher SB, Sigalov A, Benoit CR, Lee H, Lam M, Seyfried NT, Bennett DA, De Jager PL, Menon V, Young-Pearse TL. INPP5D regulates inflammasome activation in human microglia. Nat Commun 2023; 14:7552. [PMID: 38016942 PMCID: PMC10684891 DOI: 10.1038/s41467-023-42819-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023] Open
Abstract
Microglia and neuroinflammation play an important role in the development and progression of Alzheimer's disease (AD). Inositol polyphosphate-5-phosphatase D (INPP5D/SHIP1) is a myeloid-expressed gene genetically-associated with AD. Through unbiased analyses of RNA and protein profiles in INPP5D-disrupted iPSC-derived human microglia, we find that reduction in INPP5D activity is associated with molecular profiles consistent with disrupted autophagy and inflammasome activation. These findings are validated through targeted pharmacological experiments which demonstrate that reduced INPP5D activity induces the formation of the NLRP3 inflammasome, cleavage of CASP1, and secretion of IL-1β and IL-18. Further, in-depth analyses of human brain tissue across hundreds of individuals using a multi-analytic approach provides evidence that a reduction in function of INPP5D in microglia results in inflammasome activation in AD. These findings provide insights into the molecular mechanisms underlying microglia-mediated processes in AD and highlight the inflammasome as a potential therapeutic target for modulating INPP5D-mediated vulnerability to AD.
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Affiliation(s)
- Vicky Chou
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Aimee J Aylward
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Nancy Ashour
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Mariko Taga
- Center for Translational and Computational Neuroimmunology, Department of Neurology, and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Gizem Terzioglu
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Masashi Fujita
- Center for Translational and Computational Neuroimmunology, Department of Neurology, and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Seeley B Fancher
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alina Sigalov
- Center for Translational and Computational Neuroimmunology, Department of Neurology, and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Courtney R Benoit
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hyo Lee
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Matti Lam
- Center for Translational and Computational Neuroimmunology, Department of Neurology, and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory School of Medicine, Atlanta, GA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology, and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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23
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Shoob S, Buchbinder N, Shinikamin O, Gold O, Baeloha H, Langberg T, Zarhin D, Shapira I, Braun G, Habib N, Slutsky I. Deep brain stimulation of thalamic nucleus reuniens promotes neuronal and cognitive resilience in an Alzheimer's disease mouse model. Nat Commun 2023; 14:7002. [PMID: 37919286 PMCID: PMC10622498 DOI: 10.1038/s41467-023-42721-5] [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: 10/15/2022] [Accepted: 10/19/2023] [Indexed: 11/04/2023] Open
Abstract
The mechanisms that confer cognitive resilience to Alzheimer's Disease (AD) are not fully understood. Here, we describe a neural circuit mechanism underlying this resilience in a familial AD mouse model. In the prodromal disease stage, interictal epileptiform spikes (IESs) emerge during anesthesia in the CA1 and mPFC regions, leading to working memory disruptions. These IESs are driven by inputs from the thalamic nucleus reuniens (nRE). Indeed, tonic deep brain stimulation of the nRE (tDBS-nRE) effectively suppresses IESs and restores firing rate homeostasis under anesthesia, preventing further impairments in nRE-CA1 synaptic facilitation and working memory. Notably, applying tDBS-nRE during the prodromal phase in young APP/PS1 mice mitigates age-dependent memory decline. The IES rate during anesthesia in young APP/PS1 mice correlates with later working memory impairments. These findings highlight the nRE as a central hub of functional resilience and underscore the clinical promise of DBS in conferring resilience to AD pathology by restoring circuit-level homeostasis.
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Affiliation(s)
- Shiri Shoob
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Nadav Buchbinder
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Ortal Shinikamin
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Or Gold
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Halit Baeloha
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Tomer Langberg
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Daniel Zarhin
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Ilana Shapira
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Gabriella Braun
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Naomi Habib
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Inna Slutsky
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel.
- Sagol School of Neuroscience, Tel Aviv University, 69978, Tel Aviv, Israel.
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