1
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Brockie S, Zhou C, Fehlings MG. Resident immune responses to spinal cord injury: role of astrocytes and microglia. Neural Regen Res 2024; 19:1678-1685. [PMID: 38103231 PMCID: PMC10960308 DOI: 10.4103/1673-5374.389630] [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: 05/04/2023] [Revised: 09/08/2023] [Accepted: 10/18/2023] [Indexed: 12/18/2023] Open
Abstract
Spinal cord injury can be traumatic or non-traumatic in origin, with the latter rising in incidence and prevalence with the aging demographics of our society. Moreover, as the global population ages, individuals with co-existent degenerative spinal pathology comprise a growing number of traumatic spinal cord injury cases, especially involving the cervical spinal cord. This makes recovery and treatment approaches particularly challenging as age and comorbidities may limit regenerative capacity. For these reasons, it is critical to better understand the complex milieu of spinal cord injury lesion pathobiology and the ensuing inflammatory response. This review discusses microglia-specific purinergic and cytokine signaling pathways, as well as microglial modulation of synaptic stability and plasticity after injury. Further, we evaluate the role of astrocytes in neurotransmission and calcium signaling, as well as their border-forming response to neural lesions. Both the inflammatory and reparative roles of these cells have eluded our complete understanding and remain key therapeutic targets due to their extensive structural and functional roles in the nervous system. Recent advances have shed light on the roles of glia in neurotransmission and reparative injury responses that will change how interventions are directed. Understanding key processes and existing knowledge gaps will allow future research to effectively target these cells and harness their regenerative potential.
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Affiliation(s)
- Sydney Brockie
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Cindy Zhou
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Michael G. Fehlings
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery and Spine Program, Department of Surgery, University of Toronto, Toronto, ON, Canada
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2
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Ugursu B, Sah A, Sartori S, Popp O, Mertins P, Dunay IR, Kettenmann H, Singewald N, Wolf SA. Microglial sex differences in innate high anxiety and modulatory effects of minocycline. Brain Behav Immun 2024; 119:465-481. [PMID: 38552926 DOI: 10.1016/j.bbi.2024.03.035] [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: 09/12/2023] [Revised: 02/08/2024] [Accepted: 03/26/2024] [Indexed: 04/18/2024] Open
Abstract
Microglia modulate synaptic refinement in the central nervous system (CNS). We have previously shown that a mouse model with innate high anxiety-related behavior (HAB) displays higher CD68+ microglia density in the key regions of anxiety circuits compared to mice with normal anxiety-related behavior (NAB) in males, and that minocycline treatment attenuated the enhanced anxiety of HAB male. Given that a higher prevalence of anxiety is widely reported in females compared to males, little is known concerning sex differences at the cellular level. Herein, we address this by analyzing microglia heterogeneity and function in the HAB and NAB brains of both sexes. Single-cell RNA sequencing revealed ten distinct microglia clusters varied by their frequency and gene expression profile. We report striking sex differences, especially in the major microglia clusters of HABs, indicating a higher expression of genes associated with phagocytosis and synaptic engulfment in the female compared to the male. On a functional level, we show that female HAB microglia engulfed a greater amount of hippocampal vGLUT1+ excitatory synapses compared to the male. We moreover show that female HAB microglia engulfed more synaptosomes compared to the male HAB in vitro. Due to previously reported effects of minocycline on microglia, we finally administered oral minocycline to HABs of both sexes and showed a significant reduction in the engulfment of synapses by female HAB microglia. In parallel to our microglia-specific findings, we further showed an anxiolytic effect of minocycline on female HABs, which is complementary to our previous findings in the male HABs. Our study, therefore, identifies the altered function of synaptic engulfment by microglia as a potential avenue to target and resolve microglia heterogeneity in mice with innate high anxiety.
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Affiliation(s)
- Bilge Ugursu
- Psychoneuroimmunology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Experimental Ophthalmology, ChariteUniversitätsmedizin Berlin, Germany
| | - Anupam Sah
- Pharmacology and Toxicology, Institute of Pharmacy and CMBI, University of Innsbruck, Austria
| | - Simone Sartori
- Pharmacology and Toxicology, Institute of Pharmacy and CMBI, University of Innsbruck, Austria
| | - Oliver Popp
- Proteomics Platform, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin Institute of Health, Berlin, Germany
| | - Philip Mertins
- Proteomics Platform, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin Institute of Health, Berlin, Germany
| | - Ildiko R Dunay
- Institute of Inflammation and Neurodegeneration, Otto-von-Guericke-University Magdeburg, Germany
| | - Helmut Kettenmann
- Shenzhen Key Laboratory of Immunomodulation for Neurological Diseases, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Nicolas Singewald
- Pharmacology and Toxicology, Institute of Pharmacy and CMBI, University of Innsbruck, Austria
| | - Susanne A Wolf
- Psychoneuroimmunology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Experimental Ophthalmology, ChariteUniversitätsmedizin Berlin, Germany.
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3
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Barclay KM, Abduljawad N, Cheng Z, Kim MW, Zhou L, Yang J, Rustenhoven J, Mazzitelli JA, Smyth LCD, Kapadia D, Brioschi S, Beatty W, Hou J, Saligrama N, Colonna M, Yu G, Kipnis J, Li Q. An inducible genetic tool to track and manipulate specific microglial states reveals their plasticity and roles in remyelination. Immunity 2024; 57:1394-1412.e8. [PMID: 38821054 DOI: 10.1016/j.immuni.2024.05.005] [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: 08/18/2023] [Revised: 02/14/2024] [Accepted: 05/07/2024] [Indexed: 06/02/2024]
Abstract
Recent single-cell RNA sequencing studies have revealed distinct microglial states in development and disease. These include proliferative-region-associated microglia (PAMs) in developing white matter and disease-associated microglia (DAMs) prevalent in various neurodegenerative conditions. PAMs and DAMs share a similar core gene signature. However, the extent of the dynamism and plasticity of these microglial states, as well as their functional significance, remains elusive, partly due to the lack of specific tools. Here, we generated an inducible Cre driver line, Clec7a-CreERT2, that targets PAMs and DAMs in the brain parenchyma. Utilizing this tool, we profiled labeled cells during development and in several disease models, uncovering convergence and context-dependent differences in PAM and DAM gene expression. Through long-term tracking, we demonstrated microglial state plasticity. Lastly, we specifically depleted DAMs in demyelination, revealing their roles in disease recovery. Together, we provide a versatile genetic tool to characterize microglial states in CNS development and disease.
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Affiliation(s)
- Kia M Barclay
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Neuroscience Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nora Abduljawad
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Neuroscience Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Zuolin Cheng
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Min Woo Kim
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Immunology Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lu Zhou
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jin Yang
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Justin Rustenhoven
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Jose A Mazzitelli
- Neuroscience Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Leon C D Smyth
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Dvita Kapadia
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Simone Brioschi
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Wandy Beatty
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - JinChao Hou
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Naresha Saligrama
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Department of Neurology, Washington University School of Medicine in St. Louis, School of Medicine, St. Louis, MO 63110, USA; Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine in St. Louis, St. Louis, MO 63112, USA
| | - Marco Colonna
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Guoqiang Yu
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Jonathan Kipnis
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Qingyun Li
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Brain Immunology and Glia (BIG) Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, School of Medicine, St. Louis, MO 63110, USA.
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Boles J, Huarte OU, Tansey MG. Peripheral endotoxin exposure in mice activates crosstalk between phagocytes in the brain and periphery. RESEARCH SQUARE 2024:rs.3.rs-4478250. [PMID: 38883776 PMCID: PMC11177977 DOI: 10.21203/rs.3.rs-4478250/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Background Inflammation is a central process of many neurological diseases, and a growing number of studies suggest that non-brain-resident immune cells may contribute to this neuroinflammation. However, the unique contributions of specific immune cell subsets to neuroinflammation are presently unknown, and it is unclear how communication between brain-resident and non-resident immune cells underlies peripheral immune cell involvement in neuroinflammation. Methods In this study, we employed the well-established model of lipopolysaccharide (LPS)-induced neuroinflammation and captured brain-resident and non-resident immune cells from the brain and its vasculature by magnetically enriching cell suspensions from the non-perfused brain for CD45 + cells. Then, we identified immune subtype-specific neuroinflammatory processes using single-cell genomics and predicted the crosstalk between immune cell subtypes by analyzing the simultaneous expression of ligands and receptors. Results We observed a greater abundance of peripheral phagocytes associated with the brain in this model of neuroinflammation, and report that these professional phagocytes activated similar transcriptional profiles to microglia during LPS-induced neuroinflammation. And, we observed that the probable crosstalk between microglia and peripheral phagocytes was activated in this model while homotypic microglial communication was likely to be decreased. Conclusions Our novel findings reveal that microglia signaling to non-brain-resident peripheral phagocytes is preferentially triggered by peripheral inflammation, which is associated with brain infiltration of peripheral cells. Overall, our study supports the involvement of peripheral immune cells in neuroinflammation and suggests several possible molecular signaling pathways between microglia and peripheral cells that may facilitate central-peripheral crosstalk during inflammation. Examining these molecular mediators in human disease and other rodent models may reveal novel targets that modify brain health, especially in comorbidities characterized by peripheral inflammation.
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5
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Kang S, Ko EY, Andrews AE, Shin JE, Nance KJ, Barman PK, Heeger PS, Freeman WM, Benayoun BA, Goodridge HS. Microglia undergo sex-dimorphic transcriptional and metabolic rewiring during aging. J Neuroinflammation 2024; 21:150. [PMID: 38840206 PMCID: PMC11155174 DOI: 10.1186/s12974-024-03130-7] [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: 03/19/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024] Open
Abstract
Microglia, the brain's resident macrophages, maintain brain homeostasis and respond to injury and infection. During aging they undergo functional changes, but the underlying mechanisms and their contributions to neuroprotection versus neurodegeneration are unclear. Previous studies suggested that microglia are sex dimorphic, so we compared microglial aging in mice of both sexes. RNA-sequencing of hippocampal microglia revealed more aging-associated changes in female microglia than male microglia, and more sex differences in old microglia than young microglia. Pathway analyses and subsequent validation assays revealed a stronger AKT-mTOR-HIF1α-driven shift to glycolysis among old female microglia and indicated that C3a production and detection was elevated in old microglia, especially in females. Recombinant C3a induced AKT-mTOR-HIF1α signaling and increased the glycolytic and phagocytic activity of young microglia. Single cell analyses attributed the aging-associated sex dimorphism to more abundant disease-associated microglia (DAM) in old female mice than old male mice, and evaluation of an Alzheimer's Disease mouse model revealed that the metabolic and complement changes are also apparent in the context of neurodegenerative disease and are strongest in the neuroprotective DAM2 subset. Collectively, our data implicate autocrine C3a-C3aR signaling in metabolic reprogramming of microglia to neuroprotective DAM during aging, especially in females, and also in Alzheimer's Disease.
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Affiliation(s)
- Seokjo Kang
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Emily Y Ko
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Amelia E Andrews
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Juliana E Shin
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Karina J Nance
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Pijus K Barman
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Peter S Heeger
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Willard M Freeman
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, 73104, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Molecular and Computational Biology Department, Arts and Sciences, USC Dornsife College of Letters, University of Southern California, Los Angeles, CA, 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Helen S Goodridge
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
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6
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Cadena MA, Sing A, Taylor K, Jin L, Ning L, Salar Amoli M, Singh Y, Lanjewar SN, Tomov ML, Serpooshan V, Sloan SA. A 3D Bioprinted Cortical Organoid Platform for Modeling Human Brain Development. Adv Healthc Mater 2024:e2401603. [PMID: 38815975 DOI: 10.1002/adhm.202401603] [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: 05/03/2024] [Revised: 05/24/2024] [Indexed: 06/01/2024]
Abstract
The ability to promote three-dimensional (3D) self-organization of induced pluripotent stem cells into complex tissue structures called organoids presents new opportunities for the field of developmental biology. Brain organoids have been used to investigate principles of neurodevelopment and neuropsychiatric disorders and serve as a drug screening and discovery platform. However, brain organoid cultures are currently limited by a lacking ability to precisely control their extracellular environment. Here, this work employs 3D bioprinting to generate a high-throughput, tunable, and reproducible scaffold for controlling organoid development and patterning. Additionally, this approach supports the coculture of organoids and vascular cells in a custom architecture containing interconnected endothelialized channels. Printing fidelity and mechanical assessments confirm that fabricated scaffolds closely match intended design features and exhibit stiffness values reflective of the developing human brain. Using organoid growth, viability, cytoarchitecture, proliferation, and transcriptomic benchmarks, this work finds that organoids cultured within the bioprinted scaffold long-term are healthy and have expected neuroectodermal differentiation. Lastly, this work confirms that the endothelial cells (ECs) in printed channel structures can migrate toward and infiltrate into the embedded organoids. This work demonstrates a tunable 3D culturing platform that can be used to create more complex and accurate models of human brain development and underlying diseases.
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Affiliation(s)
- Melissa A Cadena
- Department of Biomedical Engineering, Emory University School of Medicine and Georgia Institute of Technology, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Anson Sing
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Kylie Taylor
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Linqi Jin
- Department of Biomedical Engineering, Emory University School of Medicine and Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Liqun Ning
- Department of Biomedical Engineering, Emory University School of Medicine and Georgia Institute of Technology, Atlanta, GA, 30322, USA
- Department of Mechanical Engineering, Cleveland State University, Cleveland, OH, 44115, USA
| | - Mehdi Salar Amoli
- Department of Biomedical Engineering, Emory University School of Medicine and Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Yamini Singh
- Department of Biomedical Engineering, Emory University School of Medicine and Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Samantha N Lanjewar
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Martin L Tomov
- Department of Biomedical Engineering, Emory University School of Medicine and Georgia Institute of Technology, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Vahid Serpooshan
- Department of Biomedical Engineering, Emory University School of Medicine and Georgia Institute of Technology, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Steven A Sloan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
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7
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Holmberg JC, Riley VA, Sokolov AM, Mukherjee S, Feliciano DM. Protocol for electroporating and isolating murine (sub)ventricular zone cells for single-nuclei omics. STAR Protoc 2024; 5:103095. [PMID: 38823010 PMCID: PMC11179414 DOI: 10.1016/j.xpro.2024.103095] [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: 01/25/2024] [Revised: 03/14/2024] [Accepted: 05/08/2024] [Indexed: 06/03/2024] Open
Abstract
In vivo genetic modification of neural stem cells is necessary to model the origins and pathogenesis of neurological disorders. Electroporation is a technique that applies a transient electrical field to direct charged molecules into living cells to genetically modify the mouse brain. Here, we provide a protocol to electroporate the neural stem cells surrounding the neonatal ventricles. We describe subsequent steps to isolate and prepare nuclei from the cells and their cellular progeny for single-nuclei omics. For complete details on the use and execution of this protocol, please refer to Riley et al.1.
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Affiliation(s)
- Jennie C Holmberg
- Department of Biological Sciences, Clemson University, Clemson, SC 29631, USA.
| | - Victoria A Riley
- Department of Biological Sciences, Clemson University, Clemson, SC 29631, USA
| | - Aidan M Sokolov
- Department of Biological Sciences, Clemson University, Clemson, SC 29631, USA
| | - Sulagna Mukherjee
- Department of Biological Sciences, Clemson University, Clemson, SC 29631, USA
| | - David M Feliciano
- Department of Biological Sciences, Clemson University, Clemson, SC 29631, USA; Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA.
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8
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Patir A, Barrington J, Szymkowiak S, Brezzo G, Straus D, Alfieri A, Lefevre L, Liu Z, Ginhoux F, Henderson NC, Horsburgh K, Ramachandran P, McColl BW. Phenotypic and spatial heterogeneity of brain myeloid cells after stroke is associated with cell ontogeny, tissue damage, and brain connectivity. Cell Rep 2024; 43:114250. [PMID: 38762882 DOI: 10.1016/j.celrep.2024.114250] [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: 08/18/2023] [Revised: 03/21/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024] Open
Abstract
Acute stroke triggers extensive changes to myeloid immune cell populations in the brain that may be targets for limiting brain damage and enhancing repair. Immunomodulatory approaches will be most effective with precise manipulation of discrete myeloid cell phenotypes in time and space. Here, we investigate how stroke alters mononuclear myeloid cell composition and phenotypes at single-cell resolution and key spatial patterns. Our results show that multiple reactive microglial states and monocyte-derived populations contribute to an extensive myeloid cell repertoire in post-stroke brains. We identify important overlaps and distinctions among different cell types/states that involve ontogeny- and spatial-related properties. Notably, brain connectivity with infarcted tissue underpins the pattern of local and remote altered cell accumulation and reactivity. Our discoveries suggest a global but anatomically governed brain myeloid cell response to stroke that comprises diverse phenotypes arising through intrinsic cell ontogeny factors interacting with exposure to spatially organized brain damage and neuro-axonal cues.
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Affiliation(s)
- Anirudh Patir
- UK Dementia Research Institute, University of Edinburgh, Edinburgh EH16 4SB, UK; Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Jack Barrington
- UK Dementia Research Institute, University of Edinburgh, Edinburgh EH16 4SB, UK; Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Stefan Szymkowiak
- UK Dementia Research Institute, University of Edinburgh, Edinburgh EH16 4SB, UK; Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Gaia Brezzo
- UK Dementia Research Institute, University of Edinburgh, Edinburgh EH16 4SB, UK; Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Dana Straus
- UK Dementia Research Institute, University of Edinburgh, Edinburgh EH16 4SB, UK; Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Alessio Alfieri
- UK Dementia Research Institute, University of Edinburgh, Edinburgh EH16 4SB, UK; Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Lucas Lefevre
- UK Dementia Research Institute, University of Edinburgh, Edinburgh EH16 4SB, UK; Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Zhaoyuan Liu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Florent Ginhoux
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Neil C Henderson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4TJ, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Karen Horsburgh
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Prakash Ramachandran
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Barry W McColl
- UK Dementia Research Institute, University of Edinburgh, Edinburgh EH16 4SB, UK; Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
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9
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Mancuso R, Fattorelli N, Martinez-Muriana A, Davis E, Wolfs L, Van Den Daele J, Geric I, Premereur J, Polanco P, Bijnens B, Preman P, Serneels L, Poovathingal S, Balusu S, Verfaillie C, Fiers M, De Strooper B. Xenografted human microglia display diverse transcriptomic states in response to Alzheimer's disease-related amyloid-β pathology. Nat Neurosci 2024; 27:886-900. [PMID: 38539015 PMCID: PMC11089003 DOI: 10.1038/s41593-024-01600-y] [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: 11/28/2022] [Accepted: 02/14/2024] [Indexed: 05/14/2024]
Abstract
Microglia are central players in Alzheimer's disease pathology but analyzing microglial states in human brain samples is challenging due to genetic diversity, postmortem delay and admixture of pathologies. To circumvent these issues, here we generated 138,577 single-cell expression profiles of human stem cell-derived microglia xenotransplanted in the brain of the AppNL-G-F model of amyloid pathology and wild-type controls. Xenografted human microglia adopt a disease-associated profile similar to that seen in mouse microglia, but display a more pronounced human leukocyte antigen or HLA state, likely related to antigen presentation in response to amyloid plaques. The human microglial response also involves a pro-inflammatory cytokine/chemokine cytokine response microglia or CRM response to oligomeric Aβ oligomers. Genetic deletion of TREM2 or APOE as well as APOE polymorphisms and TREM2R47H expression in the transplanted microglia modulate these responses differentially. The expression of other Alzheimer's disease risk genes is differentially regulated across the distinct cell states elicited in response to amyloid pathology. Thus, we have identified multiple transcriptomic cell states adopted by human microglia in a multipronged response to Alzheimer's disease-related pathology, which should be taken into account in translational studies.
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Affiliation(s)
- Renzo Mancuso
- Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium.
| | - Nicola Fattorelli
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Anna Martinez-Muriana
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Emma Davis
- UK Dementia Research Institute at UCL, University College London, London, UK
| | - Leen Wolfs
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Johanna Van Den Daele
- Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven Stem Cell Institute, Leuven, Belgium
| | - Ivana Geric
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Jessie Premereur
- Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Paula Polanco
- Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Baukje Bijnens
- Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Pranav Preman
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Lutgarde Serneels
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Suresh Poovathingal
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
| | - Sriram Balusu
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Catherine Verfaillie
- Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven Stem Cell Institute, Leuven, Belgium
| | - Mark Fiers
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
- UK Dementia Research Institute at UCL, University College London, London, UK
| | - Bart De Strooper
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium.
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium.
- UK Dementia Research Institute at UCL, University College London, London, UK.
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10
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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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11
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Shea JM, Villeda SA. MICROGLIA AGING IN THE HIPPOCAMPUS ADVANCES THROUGH INTERMEDIATE STATES THAT DRIVE INFLAMMATORY ACTIVATION AND COGNITIVE DECLINE. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588665. [PMID: 38645176 PMCID: PMC11030314 DOI: 10.1101/2024.04.09.588665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
During aging, microglia - the resident macrophages of the brain - exhibit dystrophic phenotypes and contribute to age-related neuroinflammation. While numerous hallmarks of age-related microglia dystrophy have been elucidated, the progression from homeostasis to dysfunction during the aging process remains unresolved. To bridge this gap in knowledge, we undertook complementary cellular and molecular analyses of microglia in the mouse hippocampus across the adult lifespan and in the experimental aging model of heterochronic parabiosis. Single-cell RNA-Seq and pseudotime analysis revealed age-related transcriptional heterogeneity in hippocampal microglia and identified intermediate states of microglial aging that also emerge following heterochronic parabiosis. We tested the functionality of intermediate stress response states via TGFβ1 and translational states using pharmacological approaches in vitro to reveal their modulation of the progression to an inflammatory state. Furthermore, we utilized single-cell RNA-Seq in conjunction with an in vivo adult microglia-specific Tgfb1 conditional genetic knockout mouse model, to demonstrate that microglia advancement through intermediate aging states drives inflammatory activation and associated hippocampal-dependent cognitive decline.
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Affiliation(s)
- Jeremy M. Shea
- Department of Anatomy, University of California San Francisco, San Francisco, California 94143, USA
| | - Saul A. Villeda
- Department of Anatomy, University of California San Francisco, San Francisco, California 94143, USA
- Department of Physical Therapy and Rehabilitation Science, University of California San Francisco, San Francisco, California 94143, USA
- Bakar Aging Research Institute, University of California San Francisco, San Francisco, California, 94143, USA
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12
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Wu D, Sun JKL, Chow KHM. Neuronal cell cycle reentry events in the aging brain are more prevalent in neurodegeneration and lead to cellular senescence. PLoS Biol 2024; 22:e3002559. [PMID: 38652714 PMCID: PMC11037540 DOI: 10.1371/journal.pbio.3002559] [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: 11/22/2023] [Accepted: 02/22/2024] [Indexed: 04/25/2024] Open
Abstract
Increasing evidence indicates that terminally differentiated neurons in the brain may recommit to a cell cycle-like process during neuronal aging and under disease conditions. Because of the rare existence and random localization of these cells in the brain, their molecular profiles and disease-specific heterogeneities remain unclear. Through a bioinformatics approach that allows integrated analyses of multiple single-nucleus transcriptome datasets from human brain samples, these rare cell populations were identified and selected for further characterization. Our analyses indicated that these cell cycle-related events occur predominantly in excitatory neurons and that cellular senescence is likely their immediate terminal fate. Quantitatively, the number of cell cycle re-engaging and senescent neurons decreased during the normal brain aging process, but in the context of late-onset Alzheimer's disease (AD), these cells accumulate instead. Transcriptomic profiling of these cells suggested that disease-specific differences were predominantly tied to the early stage of the senescence process, revealing that these cells presented more proinflammatory, metabolically deregulated, and pathology-associated signatures in disease-affected brains. Similarly, these general features of cell cycle re-engaging neurons were also observed in a subpopulation of dopaminergic neurons identified in the Parkinson's disease (PD)-Lewy body dementia (LBD) model. An extended analysis conducted in a mouse model of brain aging further validated the ability of this bioinformatics approach to determine the robust relationship between the cell cycle and senescence processes in neurons in this cross-species setting.
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Affiliation(s)
- Deng Wu
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jacquelyne Ka-Li Sun
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kim Hei-Man Chow
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong SAR, China
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
- Nexus of Rare Neurodegenerative Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China
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13
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Carroll KR, Mizrachi M, Simmons S, Toz B, Kowal C, Wingard J, Tehrani N, Zarfeshani A, Kello N, El Khoury L, Weissman-Tsukamoto R, Levin JZ, Volpe BT, Diamond B. Lupus autoantibodies initiate neuroinflammation sustained by continuous HMGB1:RAGE signaling and reversed by increased LAIR-1 expression. Nat Immunol 2024; 25:671-681. [PMID: 38448779 PMCID: PMC11141703 DOI: 10.1038/s41590-024-01772-6] [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: 07/07/2023] [Accepted: 01/25/2024] [Indexed: 03/08/2024]
Abstract
Cognitive impairment is a frequent manifestation of neuropsychiatric systemic lupus erythematosus, present in up to 80% of patients and leading to a diminished quality of life. In the present study, we used a model of lupus-like cognitive impairment that is initiated when antibodies that crossreact with excitatory neuronal receptors penetrate the hippocampus, causing immediate, self-limited, excitotoxic death of hippocampal neurons, which is then followed by a significant loss of dendritic complexity in surviving neurons. This injury creates a maladaptive equilibrium that is sustained in mice for at least 1 year. We identified a feedforward loop of microglial activation and microglia-dependent synapse elimination dependent on neuronal secretion of high mobility group box 1 protein (HMGB1) which binds the receptor for advanced glycation end products (RAGE) and leads to microglial secretion of C1q, upregulation of interleukin-10 with consequent downregulation of leukocyte-associated immunoglobulin-like receptor 1 (LAIR-1), an inhibitory receptor for C1q. Treatment with a centrally acting angiotensin-converting enzyme inhibitor or with an angiotensin-receptor blocker restored a healthy equilibrium, microglial quiescence and intact spatial memory.
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Affiliation(s)
- Kaitlin R Carroll
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Mark Mizrachi
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Sean Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bahtiyar Toz
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Czeslawa Kowal
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Jeffrey Wingard
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Nazila Tehrani
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Aida Zarfeshani
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | | | | | | | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bruce T Volpe
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Betty Diamond
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA.
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14
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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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15
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Jiménez-Gracia L, Marchese D, Nieto JC, Caratù G, Melón-Ardanaz E, Gudiño V, Roth S, Wise K, Ryan NK, Jensen KB, Hernando-Momblona X, Bernardes JP, Tran F, Sievers LK, Schreiber S, van den Berge M, Kole T, van der Velde PL, Nawijn MC, Rosenstiel P, Batlle E, Butler LM, Parish IA, Plummer J, Gut I, Salas A, Heyn H, Martelotto LG. FixNCut: single-cell genomics through reversible tissue fixation and dissociation. Genome Biol 2024; 25:81. [PMID: 38553769 PMCID: PMC10979608 DOI: 10.1186/s13059-024-03219-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can further increase robustness and reproducibility by avoiding artifacts introduced during specimen handling. We present FixNCut, a methodology for the reversible fixation of tissue followed by dissociation that overcomes current limitations. We applied FixNCut to human and mouse tissues to demonstrate the preservation of RNA integrity, sequencing library complexity, and cellular composition, while diminishing stress-related artifacts. Besides single-cell RNA sequencing, FixNCut is compatible with multiple single-cell and spatial technologies, making it a versatile tool for robust and flexible study designs.
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Affiliation(s)
- Laura Jiménez-Gracia
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Domenica Marchese
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Juan C Nieto
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Ginevra Caratù
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Elisa Melón-Ardanaz
- Inflammatory Bowel Disease Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Victoria Gudiño
- Inflammatory Bowel Disease Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Sara Roth
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
- Monash University Department of Surgery, Alfred Hospital, Melbourne, VIC, Australia
| | - Kellie Wise
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, Adelaide, South Australia, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia
- Australian Genomics Research Facility, Adelaide, South Australia, Australia
| | - Natalie K Ryan
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia
- Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Kirk B Jensen
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, Adelaide, South Australia, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia
- Australian Genomics Research Facility, Adelaide, South Australia, Australia
| | - Xavier Hernando-Momblona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Joana P Bernardes
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Internal Medicine I, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Laura Katharina Sievers
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Internal Medicine I, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Internal Medicine I, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Maarten van den Berge
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Tessa Kole
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Petra L van der Velde
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Lisa M Butler
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia
- Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Jasmine Plummer
- St Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ivo Gut
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Azucena Salas
- Inflammatory Bowel Disease Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain.
- Universitat de Barcelona (UB), Barcelona, Spain.
- Omniscope, Barcelona, Spain.
| | - Luciano G Martelotto
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, Adelaide, South Australia, Australia.
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia.
- Omniscope, Barcelona, Spain.
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16
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Passino R, Finneran MC, Hafner H, Feng Q, Huffman LD, Zhao XF, Johnson CN, Kawaguchi R, Oses-Prieto JA, Burlingame AL, Geschwind DH, Benowitz LI, Giger RJ. Neutrophil-inflicted vasculature damage suppresses immune-mediated optic nerve regeneration. Cell Rep 2024; 43:113931. [PMID: 38492223 DOI: 10.1016/j.celrep.2024.113931] [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: 09/24/2023] [Revised: 01/03/2024] [Accepted: 02/21/2024] [Indexed: 03/18/2024] Open
Abstract
In adult mammals, injured retinal ganglion cells (RGCs) fail to spontaneously regrow severed axons, resulting in permanent visual deficits. Robust axon growth, however, is observed after intra-ocular injection of particulate β-glucan isolated from yeast. Blood-borne myeloid cells rapidly respond to β-glucan, releasing numerous pro-regenerative factors. Unfortunately, the pro-regenerative effects are undermined by retinal damage inflicted by an overactive immune system. Here, we demonstrate that protection of the inflamed vasculature promotes immune-mediated RGC regeneration. In the absence of microglia, leakiness of the blood-retina barrier increases, pro-inflammatory neutrophils are elevated, and RGC regeneration is reduced. Functional ablation of the complement receptor 3 (CD11b/integrin-αM), but not the complement components C1q-/- or C3-/-, reduces ocular inflammation, protects the blood-retina barrier, and enhances RGC regeneration. Selective targeting of neutrophils with anti-Ly6G does not increase axogenic neutrophils but protects the blood-retina barrier and enhances RGC regeneration. Together, these findings reveal that protection of the inflamed vasculature promotes neuronal regeneration.
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Affiliation(s)
- Ryan Passino
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Matthew C Finneran
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Hannah Hafner
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Qian Feng
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lucas D Huffman
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Xiao-Feng Zhao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Craig N Johnson
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Riki Kawaguchi
- Departments of Psychiatry and Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Program in Neurogenetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Juan A Oses-Prieto
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA
| | - Alma L Burlingame
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA
| | - Daniel H Geschwind
- Departments of Psychiatry and Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Program in Neurogenetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute of Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Larry I Benowitz
- Departments of Neurosurgery and Ophthalmology, Harvard Medical School, Boston, MA 02115, USA; Department of Neurosurgery, Boston Children's Hospital, Boston MA 02115, USA; Departmant of Ophthalmology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Roman J Giger
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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17
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Childs JE, Morabito S, Das S, Santelli C, Pham V, Kusche K, Vera VA, Reese F, Campbell RR, Matheos DP, Swarup V, Wood MA. Relapse to cocaine seeking is regulated by medial habenula NR4A2/NURR1 in mice. Cell Rep 2024; 43:113956. [PMID: 38489267 PMCID: PMC11100346 DOI: 10.1016/j.celrep.2024.113956] [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: 09/28/2022] [Revised: 09/11/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Drugs of abuse can persistently change the reward circuit in ways that contribute to relapse behavior, partly via mechanisms that regulate chromatin structure and function. Nuclear orphan receptor subfamily4 groupA member2 (NR4A2, also known as NURR1) is an important effector of histone deacetylase 3 (HDAC3)-dependent mechanisms in persistent memory processes and is highly expressed in the medial habenula (MHb), a region that regulates nicotine-associated behaviors. Here, expressing the Nr4a2 dominant negative (Nurr2c) in the MHb blocks reinstatement of cocaine seeking in mice. We use single-nucleus transcriptomics to characterize the molecular cascade following Nr4a2 manipulation, revealing changes in transcriptional networks related to addiction, neuroplasticity, and GABAergic and glutamatergic signaling. The network controlled by NR4A2 is characterized using a transcription factor regulatory network inference algorithm. These results identify the MHb as a pivotal regulator of relapse behavior and demonstrate the importance of NR4A2 as a key mechanism driving the MHb component of relapse.
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Affiliation(s)
- Jessica E Childs
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Samuel Morabito
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA 92697, USA; Mathematical, Computational, and Systems Biology (MCSB) Program, University of California, Irvine, Irvine, CA 92697, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Sudeshna Das
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA 92697, USA
| | - Caterina Santelli
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Victoria Pham
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Kelly Kusche
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Vanessa Alizo Vera
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Fairlie Reese
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Rianne R Campbell
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Dina P Matheos
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA 92697, USA.
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA 92697, USA.
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18
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Joshi R, Brezani V, Mey GM, Guixé-Muntet S, Ortega-Ribera M, Zhuang Y, Zivny A, Werneburg S, Gracia-Sancho J, Szabo G. IRF3 regulates neuroinflammatory responses and the expression of genes associated with Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.582968. [PMID: 38654824 PMCID: PMC11037866 DOI: 10.1101/2024.03.08.582968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The pathological role of interferon signaling is emerging in neuroinflammatory disorders, yet, the specific role of Interferon Regulatory Factor 3 (IRF3) in neuroinflammation remains poorly understood. Here, we show that global IRF3 deficiency delays TLR4-mediated signaling in microglia and attenuates the hallmark features of LPS-induced inflammation such as cytokine release, microglial reactivity, astrocyte activation, myeloid cell infiltration, and inflammasome activation. Moreover, expression of a constitutively active IRF3 (S388D/S390D:IRF3-2D) in microglia induces a transcriptional program reminiscent of the Activated Response Microglia and the expression of genes associated with Alzheimer's Disease, notably apolipoprotein-e. Lastly, using bulk-RNAseq of IRF3-2D brain myeloid cells, we identified Z-DNA binding protein-1 as a target of IRF3 that is relevant across various neuroinflammatory disorders. Together, our results identify IRF3 as an important regulator of LPS-mediated neuroinflammatory responses and highlight IRF3 as a central regulator of disease-specific gene activation in different neuroinflammatory diseases.
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Affiliation(s)
- Radhika Joshi
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, USA
| | - Veronika Brezani
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, USA
| | - Gabrielle M Mey
- Department of Opthalmology and Visual Sciences, Kellogg Eye Center Michigan Neuroscience Institute, University of Michigan, Ann Arbor, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Sergi Guixé-Muntet
- Liver Vascular Biology, IDIBAPS Biomedical Research Institute- CIBEREHD, Barcelona, Spain
| | - Marti Ortega-Ribera
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, USA
| | - Yuan Zhuang
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, USA
| | - Adam Zivny
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, USA
| | - Sebastian Werneburg
- Department of Opthalmology and Visual Sciences, Kellogg Eye Center Michigan Neuroscience Institute, University of Michigan, Ann Arbor, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jordi Gracia-Sancho
- Liver Vascular Biology, IDIBAPS Biomedical Research Institute- CIBEREHD, Barcelona, Spain
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Gyongyi Szabo
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, USA
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19
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Huang S, Dong W, Lin X, Xu K, Li K, Xiong S, Wang Z, Nie X, Bian JS. Disruption of the Na +/K +-ATPase-purinergic P2X7 receptor complex in microglia promotes stress-induced anxiety. Immunity 2024; 57:495-512.e11. [PMID: 38395698 DOI: 10.1016/j.immuni.2024.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 11/15/2023] [Accepted: 01/29/2024] [Indexed: 02/25/2024]
Abstract
Na+/K+-ATPase (NKA) plays an important role in the central nervous system. However, little is known about its function in the microglia. Here, we found that NKAα1 forms a complex with the purinergic P2X7 receptor (P2X7R), an adenosine 5'-triphosphate (ATP)-gated ion channel, under physiological conditions. Chronic stress or treatment with lipopolysaccharide plus ATP decreased the membrane expression of NKAα1 in microglia, facilitated P2X7R function, and promoted microglia inflammatory activation via activation of the NLRP3 inflammasome. Accordingly, global deletion or conditional deletion of NKAα1 in microglia under chronic stress-induced aggravated anxiety-like behavior and neuronal hyperexcitability. DR5-12D, a monoclonal antibody that stabilizes membrane NKAα1, improved stress-induced anxiety-like behavior and ameliorated neuronal hyperexcitability and neurogenesis deficits in the ventral hippocampus of mice. Our results reveal that NKAα1 limits microglia inflammation and may provide a target for the treatment of stress-related neuroinflammation and diseases.
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Affiliation(s)
- Songqiang Huang
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Wanting Dong
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Xiaoqian Lin
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Kangtai Xu
- Department of Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Kun Li
- Department of Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Siping Xiong
- Department of Pathology, the Eighth Affiliated Hospital of Sun Yat-Sen University, Shenzhen 518033, Guangdong, China
| | - Zilong Wang
- Department of Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Xiaowei Nie
- Key Laboratory of Shenzhen Respiratory Disease, Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (the First Affiliated Hospital of Southern University of Science and Technology, the Second Clinical Medical College of Jinan University), Shenzhen 518020, Guangdong, China.
| | - Jin-Song Bian
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
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20
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Kwok AJ, Lu J, Huang J, Ip BY, Mok VCT, Lai HM, Ko H. High-resolution omics of vascular ageing and inflammatory pathways in neurodegeneration. Semin Cell Dev Biol 2024; 155:30-49. [PMID: 37380595 DOI: 10.1016/j.semcdb.2023.06.005] [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: 04/29/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023]
Abstract
High-resolution omics, particularly single-cell and spatial transcriptomic profiling, are rapidly enhancing our comprehension of the normal molecular diversity of gliovascular cells, as well as their age-related changes that contribute to neurodegeneration. With more omic profiling studies being conducted, it is becoming increasingly essential to synthesise valuable information from the rapidly accumulating findings. In this review, we present an overview of the molecular features of neurovascular and glial cells that have been recently discovered through omic profiling, with a focus on those that have potentially significant functional implications and/or show cross-species differences between human and mouse, and that are linked to vascular deficits and inflammatory pathways in ageing and neurodegenerative disorders. Additionally, we highlight the translational applications of omic profiling, and discuss omic-based strategies to accelerate biomarker discovery and facilitate disease course-modifying therapeutics development for neurodegenerative conditions.
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Affiliation(s)
- Andrew J Kwok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Jianning Lu
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Junzhe Huang
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Bonaventure Y Ip
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Vincent C T Mok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hei Ming Lai
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Ho Ko
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
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21
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You Y, Chen Z, Hu WW. The role of microglia heterogeneity in synaptic plasticity and brain disorders: Will sequencing shed light on the discovery of new therapeutic targets? Pharmacol Ther 2024; 255:108606. [PMID: 38346477 DOI: 10.1016/j.pharmthera.2024.108606] [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: 10/31/2023] [Revised: 01/05/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Microglia play a crucial role in interacting with neuronal synapses and modulating synaptic plasticity. This function is particularly significant during postnatal development, as microglia are responsible for removing excessive synapses to prevent neurodevelopmental deficits. Dysregulation of microglial synaptic function has been well-documented in various pathological conditions, notably Alzheimer's disease and multiple sclerosis. The recent application of RNA sequencing has provided a powerful and unbiased means to decipher spatial and temporal microglial heterogeneity. By identifying microglia with varying gene expression profiles, researchers have defined multiple subgroups of microglia associated with specific pathological states, including disease-associated microglia, interferon-responsive microglia, proliferating microglia, and inflamed microglia in multiple sclerosis, among others. However, the functional roles of these distinct subgroups remain inadequately characterized. This review aims to refine our current understanding of the potential roles of heterogeneous microglia in regulating synaptic plasticity and their implications for various brain disorders, drawing from recent sequencing research and functional studies. This knowledge may aid in the identification of pathogenetic biomarkers and potential factors contributing to pathogenesis, shedding new light on the discovery of novel drug targets. The field of sequencing-based data mining is evolving toward a multi-omics approach. With advances in viral tools for precise microglial regulation and the development of brain organoid models, we are poised to elucidate the functional roles of microglial subgroups detected through sequencing analysis, ultimately identifying valuable therapeutic targets.
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Affiliation(s)
- Yi You
- Department of Pharmacology and Department of Pharmacy of the Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhong Chen
- Department of Pharmacology and Department of Pharmacy of the Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China; Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Wei-Wei Hu
- Department of Pharmacology and Department of Pharmacy of the Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China.
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22
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Benkő S, Dénes Á. Microglial Inflammatory Mechanisms in Stroke: The Jury Is Still Out. Neuroscience 2024:S0306-4522(24)00057-5. [PMID: 38364965 DOI: 10.1016/j.neuroscience.2024.02.007] [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: 01/04/2024] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
Microglia represent the main immune cell population in the CNS with unique homeostatic roles and contribution to broad neurological conditions. Stroke is associated with marked changes in microglial phenotypes and induction of inflammatory responses, which emerge as key modulators of brain injury, neurological outcome and regeneration. However, due to the limited availability of functional studies with selective targeting of microglia and microglia-related inflammatory pathways in stroke, the vast majority of observations remain correlative and controversial. Because extensive review articles discussing the role of inflammatory mechanisms in different forms of acute brain injury are available, here we focus on some specific pathways that appear to be important for stroke pathophysiology with assumed contribution by microglia. While the growing toolkit for microglia manipulation increasingly allows targeting inflammatory pathways in a cell-specific manner, reconsideration of some effects devoted to microglia may also be required. This may particularly concern the interpretation of inflammatory mechanisms that emerge in response to stroke as a form of sterile injury and change markedly in chronic inflammation and common stroke comorbidities.
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Affiliation(s)
- Szilvia Benkő
- Laboratory of Inflammation-Physiology, Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - Ádám Dénes
- "Momentum" Laboratory of Neuroimmunology, Institute of Experimental Medicine, Budapest H-1083, Hungary.
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23
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Lund H, Hunt MA, Kurtović Z, Sandor K, Kägy PB, Fereydouni N, Julien A, Göritz C, Vazquez-Liebanas E, Andaloussi Mäe M, Jurczak A, Han J, Zhu K, Harris RA, Lampa J, Graversen JH, Etzerodt A, Haglund L, Yaksh TL, Svensson CI. CD163+ macrophages monitor enhanced permeability at the blood-dorsal root ganglion barrier. J Exp Med 2024; 221:e20230675. [PMID: 38117255 PMCID: PMC10733632 DOI: 10.1084/jem.20230675] [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: 04/20/2023] [Revised: 10/04/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
In dorsal root ganglia (DRG), macrophages reside close to sensory neurons and have largely been explored in the context of pain, nerve injury, and repair. However, we discovered that most DRG macrophages interact with and monitor the vasculature by sampling macromolecules from the blood. Characterization of the DRG vasculature revealed a specialized endothelial bed that transformed in molecular, structural, and permeability properties along the arteriovenous axis and was covered by macrophage-interacting pericytes and fibroblasts. Macrophage phagocytosis spatially aligned with peak endothelial permeability, a process regulated by enhanced caveolar transcytosis in endothelial cells. Profiling the DRG immune landscape revealed two subsets of perivascular macrophages with distinct transcriptome, turnover, and function. CD163+ macrophages self-maintained locally, specifically participated in vasculature monitoring, displayed distinct responses during peripheral inflammation, and were conserved in mouse and man. Our work provides a molecular explanation for the permeability of the blood-DRG barrier and identifies an unappreciated role of macrophages as integral components of the DRG-neurovascular unit.
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Affiliation(s)
- Harald Lund
- Department of Physiology and Pharmacology, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Matthew A. Hunt
- Department of Physiology and Pharmacology, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Zerina Kurtović
- Department of Physiology and Pharmacology, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Kancera AB, Karolinska Institutet Science Park, Stockholm, Sweden
| | - Katalin Sandor
- Department of Physiology and Pharmacology, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paul B. Kägy
- Department of Physiology and Pharmacology, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Noah Fereydouni
- Department of Medicine, Rheumatology Unit, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anais Julien
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christian Göritz
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Elisa Vazquez-Liebanas
- Department of Immunology, Genetics, and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Maarja Andaloussi Mäe
- Department of Immunology, Genetics, and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Alexandra Jurczak
- Department of Physiology and Pharmacology, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jinming Han
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Keying Zhu
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Robert A. Harris
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jon Lampa
- Department of Medicine, Rheumatology Unit, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Anders Etzerodt
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Lisbet Haglund
- Division of Orthopaedic Surgery, Department of Surgery, McGill University, Montreal, Canada
| | - Tony L. Yaksh
- Department of Anesthesiology, University of California, San Diego, CA, USA
| | - Camilla I. Svensson
- Department of Physiology and Pharmacology, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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24
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Company C, Schmitt MJ, Dramaretska Y, Serresi M, Kertalli S, Jiang B, Yin JA, Aguzzi A, Barozzi I, Gargiulo G. Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes. Nat Commun 2024; 15:897. [PMID: 38316783 PMCID: PMC10844330 DOI: 10.1038/s41467-024-45069-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Descriptive data are rapidly expanding in biomedical research. Instead, functional validation methods with sufficient complexity remain underdeveloped. Transcriptional reporters allow experimental characterization and manipulation of developmental and disease cell states, but their design lacks flexibility. Here, we report logical design of synthetic cis-regulatory DNA (LSD), a computational framework leveraging phenotypic biomarkers and trans-regulatory networks as input to design reporters marking the activity of selected cellular states and pathways. LSD uses bulk or single-cell biomarkers and a reference genome or custom cis-regulatory DNA datasets with user-defined boundary regions. By benchmarking validated reporters, we integrate LSD with a computational ranking of phenotypic specificity of putative cis-regulatory DNA. Experimentally, LSD-designed reporters targeting a wide range of cell states are functional without minimal promoters. Applied to broadly expressed genes from human and mouse tissues, LSD generates functional housekeeper-like sLCRs compatible with size constraints of AAV vectors for gene therapy applications. A mesenchymal glioblastoma reporter designed by LSD outperforms previously validated ones and canonical cell surface markers. In genome-scale CRISPRa screens, LSD facilitates the discovery of known and novel bona fide cell-state drivers. Thus, LSD captures core principles of cis-regulation and is broadly applicable to studying complex cell states and mechanisms of transcriptional regulation.
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Affiliation(s)
- Carlos Company
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Matthias Jürgen Schmitt
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Yuliia Dramaretska
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Michela Serresi
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Sonia Kertalli
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Ben Jiang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Jiang-An Yin
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Gaetano Gargiulo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany.
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25
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He Z, Chen Q, Wang K, Lin J, Peng Y, Zhang J, Yan X, Jie Y. Single-cell transcriptomics analysis of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. Eur J Neurosci 2024; 59:333-357. [PMID: 38221677 DOI: 10.1111/ejn.16242] [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: 05/17/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 01/16/2024]
Abstract
Single-cell transcriptomics analysis is an advanced technology that can describe the intracellular transcriptome in complex tissues. It profiles and analyses datasets by single-cell RNA sequencing. Neurodegenerative diseases are identified by the abnormal apoptosis of neurons in the brain with few or no effective therapy strategies at present, which has been a growing healthcare concern and brought a great burden to society. The transcriptome of individual cells provides deep insights into previously unforeseen cellular heterogeneity and gene expression differences in neurodegenerative disorders. It detects multiple cell subsets and functional changes during pathological progression, which deepens the understanding of the molecular underpinnings and cellular basis of neurodegenerative diseases. Furthermore, the transcriptome analysis of immune cells shows the regulation of immune response. Different subtypes of immune cells and their interaction are found to contribute to disease progression. This finding enables the discovery of novel targets and biomarkers for early diagnosis. In this review, we emphasize the principles of the technology, and its recent progress in the study of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. The application of single-cell transcriptomics analysis in neurodegenerative disorders would help explore the pathogenesis of these diseases and develop novel therapeutic methods.
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Affiliation(s)
- Ziping He
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Qianqian Chen
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Kaiyue Wang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiang Lin
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Yilin Peng
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Jinlong Zhang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
| | - Xisheng Yan
- Department of Cardiovascular Medicine, Wuhan Third Hospital & Tongren Hospital of Wuhan University, Wuhan, China
| | - Yan Jie
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
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26
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Balak CD, Han CZ, Glass CK. Deciphering microglia phenotypes in health and disease. Curr Opin Genet Dev 2024; 84:102146. [PMID: 38171044 DOI: 10.1016/j.gde.2023.102146] [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: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024]
Abstract
Microglia are the major immune cells of the central nervous system (CNS) that perform numerous adaptive functions required for normal CNS development and homeostasis but are also linked to neurodegenerative and behavioral diseases. Microglia development and function are strongly influenced by brain environmental signals that are integrated at the level of transcriptional enhancers to drive specific programs of gene expression. Here, we describe a conceptual framework for how lineage-determining and signal-dependent transcription factors interact to select and regulate the ensembles of enhancers that determine microglia development and function. We then highlight recent findings that advance these concepts and conclude with a consideration of open questions that represent some of the major hurdles to be addressed in the future.
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Affiliation(s)
- Christopher D Balak
- Department of Cellular and Molecular Medicine, University of California, San Diego, USA; Biomedical Sciences Graduate Program, University of California, San Diego, USA
| | - Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, USA; Department of Medicine, University of California, San Diego, USA.
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27
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Etebar F, Harkin DG, White AR, Dando SJ. Non-invasive in vivo imaging of brain and retinal microglia in neurodegenerative diseases. Front Cell Neurosci 2024; 18:1355557. [PMID: 38348116 PMCID: PMC10859418 DOI: 10.3389/fncel.2024.1355557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/10/2024] [Indexed: 02/15/2024] Open
Abstract
Microglia play crucial roles in immune responses and contribute to fundamental biological processes within the central nervous system (CNS). In neurodegenerative diseases, microglia undergo functional changes and can have both protective and pathogenic roles. Microglia in the retina, as an extension of the CNS, have also been shown to be affected in many neurological diseases. While our understanding of how microglia contribute to pathological conditions is incomplete, non-invasive in vivo imaging of brain and retinal microglia in living subjects could provide valuable insights into their role in the neurodegenerative diseases and open new avenues for diagnostic biomarkers. This mini-review provides an overview of the current brain and retinal imaging tools for studying microglia in vivo. We focus on microglia targets, the advantages and limitations of in vivo microglia imaging approaches, and applications for evaluating the pathogenesis of neurological conditions, such as Alzheimer's disease and multiple sclerosis.
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Affiliation(s)
- Fazeleh Etebar
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Damien G. Harkin
- Centre for Vision and Eye Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Anthony R. White
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Samantha J. Dando
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Vision and Eye Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT), Brisbane, QLD, Australia
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28
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Srinivasan S, Kancheva D, De Ren S, Saito T, Jans M, Boone F, Vandendriessche C, Paesmans I, Maurin H, Vandenbroucke RE, Hoste E, Voet S, Scheyltjens I, Pavie B, Lippens S, Schwabenland M, Prinz M, Saido T, Bottelbergs A, Movahedi K, Lamkanfi M, van Loo G. Inflammasome signaling is dispensable for ß-amyloid-induced neuropathology in preclinical models of Alzheimer's disease. Front Immunol 2024; 15:1323409. [PMID: 38352874 PMCID: PMC10863058 DOI: 10.3389/fimmu.2024.1323409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024] Open
Abstract
Background Alzheimer's disease (AD) is the most common neurodegenerative disorder affecting memory and cognition. The disease is accompanied by an abnormal deposition of ß-amyloid plaques in the brain that contributes to neurodegeneration and is known to induce glial inflammation. Studies in the APP/PS1 mouse model of ß-amyloid-induced neuropathology have suggested a role for inflammasome activation in ß-amyloid-induced neuroinflammation and neuropathology. Methods Here, we evaluated the in vivo role of microglia-selective and full body inflammasome signalling in several mouse models of ß-amyloid-induced AD neuropathology. Results Microglia-specific deletion of the inflammasome regulator A20 and inflammasome effector protease caspase-1 in the AppNL-G-F and APP/PS1 models failed to identify a prominent role for microglial inflammasome signalling in ß-amyloid-induced neuropathology. Moreover, global inflammasome inactivation through respectively full body deletion of caspases 1 and 11 in AppNL-G-F mice and Nlrp3 deletion in APP/PS1 mice also failed to modulate amyloid pathology and disease progression. In agreement, single-cell RNA sequencing did not reveal an important role for Nlrp3 signalling in driving microglial activation and the transition into disease-associated states, both during homeostasis and upon amyloid pathology. Conclusion Collectively, these results question a generalizable role for inflammasome activation in preclinical amyloid-only models of neuroinflammation.
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Affiliation(s)
- Sahana Srinivasan
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Daliya Kancheva
- Brain and Systems Immunology Lab, Brussels Center for Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sofie De Ren
- Neuroscience Therapeutic Area, Janssen Research and Development, Beerse, Belgium
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Saitama, Japan
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Maude Jans
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Fleur Boone
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Charysse Vandendriessche
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Ine Paesmans
- Neuroscience Therapeutic Area, Janssen Research and Development, Beerse, Belgium
| | - Hervé Maurin
- Neuroscience Therapeutic Area, Janssen Research and Development, Beerse, Belgium
| | - Roosmarijn E. Vandenbroucke
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Esther Hoste
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Sofie Voet
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Isabelle Scheyltjens
- Brain and Systems Immunology Lab, Brussels Center for Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Benjamin Pavie
- VIB Center for Inflammation Research, Ghent, Belgium
- VIB Bioimaging Core, Ghent, Belgium
| | - Saskia Lippens
- VIB Center for Inflammation Research, Ghent, Belgium
- VIB Bioimaging Core, Ghent, Belgium
| | - Marius Schwabenland
- Institute of Neuropathology Medical Center, University of Freiburg, Freiburg, Germany
| | - Marco Prinz
- Institute of Neuropathology Medical Center, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Takaomi Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Saitama, Japan
| | - Astrid Bottelbergs
- Neuroscience Therapeutic Area, Janssen Research and Development, Beerse, Belgium
| | - Kiavash Movahedi
- Brain and Systems Immunology Lab, Brussels Center for Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mohamed Lamkanfi
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Geert van Loo
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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29
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Bedolla AM, McKinsey GL, Ware K, Santander N, Arnold TD, Luo Y. A comparative evaluation of the strengths and potential caveats of the microglial inducible CreER mouse models. Cell Rep 2024; 43:113660. [PMID: 38217856 PMCID: PMC10874587 DOI: 10.1016/j.celrep.2023.113660] [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: 04/14/2023] [Revised: 10/02/2023] [Accepted: 12/20/2023] [Indexed: 01/15/2024] Open
Abstract
The recent proliferation of new Cre and CreER recombinase lines provides researchers with a diverse toolkit to study microglial gene function. To determine how best to apply these lines in studies of microglial gene function, a thorough and detailed comparison of their properties is needed. Here, we examined four different microglial CreER lines (Cx3cr1YFP-CreER(Litt), Cx3cr1CreER(Jung), P2ry12CreER, and Tmem119CreER), focusing on (1) recombination specificity, (2) leakiness (the degree of tamoxifen-independent recombination in microglia and other cells), (3) the efficiency of tamoxifen-induced recombination, (4) extraneural recombination (the degree of recombination in cells outside of the CNS, particularly myelo/monocyte lineages), and (5) off-target effects in the context of neonatal brain development. We identify important caveats and strengths for these lines, which will provide broad significance for researchers interested in performing conditional gene deletion in microglia. We also provide data emphasizing the potential of these lines for injury models that result in the recruitment of splenic immune cells.
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Affiliation(s)
- Alicia M Bedolla
- Department of Molecular and Cellular Biosciences, University of Cincinnati, Cincinnati, OH 45229, USA; Neuroscience Graduate Program, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Gabriel L McKinsey
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kierra Ware
- Department of Molecular and Cellular Biosciences, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Nicolas Santander
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Rancagua, Chile
| | - Thomas D Arnold
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yu Luo
- Department of Molecular and Cellular Biosciences, University of Cincinnati, Cincinnati, OH 45229, USA; Neuroscience Graduate Program, University of Cincinnati, Cincinnati, OH 45229, USA; Immunology Graduate Program, Cincinnati Children's Hospital Medical Center.
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30
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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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31
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Weng Y, Chen N, Zhang R, He J, Ding X, Cheng G, Bi Q, Lu YM, Shen XZ, Wan S, Shi P. An integral blood-brain barrier in adulthood relies on microglia-derived PDGFB. Brain Behav Immun 2024; 115:705-717. [PMID: 37992789 DOI: 10.1016/j.bbi.2023.11.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 11/16/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
Pericyte is an indispensable cellular constituent of blood-brain barrier (BBB) and its homeostasis heavily rely on PDGFB-PDGFRβ signaling. However, the primary cellular sources of PDGFB in the central nervous system (CNS) are unclear. Microglia is not considered a component of BBB and its role in maintaining BBB integrity in steady state is controversial. In this study, by analyzing transcriptomic data and performing in situ hybridization, we revealed a transition of the primary central PDGFB producers from endothelial cells in newborns to microglia in adults. Acute loss of microglial PDGFB profoundly impaired BBB integrity in adult but not newborn mice, and thus, adult mice deficient of microglial PDGFB could not survive from a sublethal endotoxin challenge due to rampant microhemorrhages in the CNS. In contrast, acute abrogation of endothelial PDGFB had minimal effects on the BBB of adult mice but led to a severe impairment of CNS vasculature in the neonates. Moreover, we found that microglia would respond to a variety of BBB insults by upregulating PDGFB expression. These findings underscore the physiological importance of the microglia-derived PDGFB to the BBB integrity of adult mice both in steady state and under injury.
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Affiliation(s)
- Yuancheng Weng
- Department of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ningting Chen
- Department of Cardiology of the Second Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Rui Zhang
- Brain Center, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Jian He
- Brain Center, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xukai Ding
- Department of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Guo Cheng
- Department of Cardiology of the Second Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qianqian Bi
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Ying-Mei Lu
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiao Z Shen
- Department of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Brain Center, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Shu Wan
- Brain Center, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
| | - Peng Shi
- Department of Cardiology of the Second Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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32
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Wallace JL, Pollen AA. Human neuronal maturation comes of age: cellular mechanisms and species differences. Nat Rev Neurosci 2024; 25:7-29. [PMID: 37996703 DOI: 10.1038/s41583-023-00760-3] [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: 10/12/2023] [Indexed: 11/25/2023]
Abstract
The delayed and prolonged postmitotic maturation of human neurons, compared with neurons from other species, may contribute to human-specific cognitive abilities and neurological disorders. Here we review the mechanisms of neuronal maturation, applying lessons from model systems to understand the specific features of protracted human cortical maturation and species differences. We cover cell-intrinsic features of neuronal maturation, including transcriptional, epigenetic and metabolic mechanisms, as well as cell-extrinsic features, including the roles of activity and synapses, the actions of glial cells and the contribution of the extracellular matrix. We discuss evidence for species differences in biochemical reaction rates, the proposed existence of an epigenetic maturation clock and the contributions of both general and modular mechanisms to species-specific maturation timing. Finally, we suggest approaches to measure, improve and accelerate the maturation of human neurons in culture, examine crosstalk and interactions among these different aspects of maturation and propose conceptual models to guide future studies.
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Affiliation(s)
- Jenelle L Wallace
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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Plaza-Zabala A, Sierra A. Studying Autophagy in Microglia: Overcoming the Obstacles. Methods Mol Biol 2024; 2713:45-70. [PMID: 37639114 DOI: 10.1007/978-1-0716-3437-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
In this chapter, we provide an overview of the main techniques and experimental approaches that can be used to analyze autophagy flux in microglia, the brain-resident macrophages. For this purpose, we first briefly introduce the main peculiarities of microglial biology, describe the basic mechanisms and functions of autophagy, and summarize the evidence accumulated so far on the role of autophagy in the regulation of microglial survival and functions, mainly phagocytosis and inflammation. Then, we highlight conceptual and technical aspects of autophagic recycling and microglial physiology that need to be taken into account for the accurate evaluation of autophagy flux in microglia. Finally, we describe the main assays that can be used to analyze the complete sequence of autophagosome formation and degradation or autophagy flux, mainly in cultured microglia and in vivo. The main approaches include indirect tracking of autophagosomes by autophagic enzymes such as LC3 by western blot and fluorescence-based confocal microscopy, as well as direct analysis of autophagic vesicles by electron microscopy. We also discuss the advantages and disadvantages of using these methods in specific experimental contexts and highlight the need to complement LC3 and/or electron microscopy data with analysis of other autophagic effectors and lysosomal proteins that participate in the initiation and completion of autophagy flux, respectively. In summary, we provide an experimental guide for the analysis of autophagosome turnover in microglia, emphasizing the need to combine as many markers and complementary approaches as possible to fully characterize the status of autophagy flux in microglia.
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Affiliation(s)
- Ainhoa Plaza-Zabala
- Achucarro Basque Center for Neuroscience, Leioa, Spain.
- Department of Pharmacology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Amanda Sierra
- Achucarro Basque Center for Neuroscience, Leioa, Spain
- Department of Neurosciences, University of the Basque Country (UPV/EHU), Leioa, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Ikerbasque Foundation, Bilbao, Spain
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Kim JS, Haimon Z, Boura-Halfon S, Jung S. Translatome Profiling of Tissue-Resident Macrophages Using the RiboTag Approach. Methods Mol Biol 2024; 2713:253-267. [PMID: 37639128 DOI: 10.1007/978-1-0716-3437-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Global gene expression profiling has provided valuable insights into the specific contributions of different cell types to various physiological processes. Notably though, both bulk and single-cell transcriptomics require the prior retrieval of the cells from their tissue context to be analyzed. Isolation protocols for tissue macrophages are, however, notoriously inefficient and, moreover, prone to introduce considerable bias and artifacts. Here, we will discuss a valuable alternative, originally introduced by Amieux and colleagues. This so-called RiboTag approach allows, in combination with respective macrophage-specific Cre transgenic lines, to retrieve macrophage translatomes from crude tissue extracts. We will review our experience with this ingenious method, focusing on the study of brain macrophages, including microglia and border-associated cells. We will elaborate on the advantages of the RiboTag approach that render it a valuable complement to standard cell sorting-based profiling strategies, especially for the investigation of tissue macrophages.
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Affiliation(s)
- Jung-Seok Kim
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Zhana Haimon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sigalit Boura-Halfon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Steffen Jung
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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35
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Bordt EA, Moya HA, Jo YC, Ravichandran CT, Bankowski IM, Ceasrine AM, McDougle CJ, Carlezon WA, Bilbo SD. Gonadal hormones impart male-biased behavioral vulnerabilities to immune activation via microglial mitochondrial function. Brain Behav Immun 2024; 115:680-695. [PMID: 37972878 PMCID: PMC10996880 DOI: 10.1016/j.bbi.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/16/2023] [Accepted: 11/11/2023] [Indexed: 11/19/2023] Open
Abstract
There is a strong male bias in the prevalence of many neurodevelopmental disorders such as autism spectrum disorder. However, the mechanisms underlying this sex bias remain elusive. Infection during the perinatal period is associated with an increased risk of neurodevelopmental disorder development. Here, we used a mouse model of early-life immune activation that reliably induces deficits in social behaviors only in males. We demonstrate that male-biased alterations in social behavior are dependent upon microglial immune signaling and are coupled to alterations in mitochondrial morphology, gene expression, and function specifically within microglia, the innate immune cells of the brain. Additionally, we show that this behavioral and microglial mitochondrial vulnerability to early-life immune activation is programmed by the male-typical perinatal gonadal hormone surge. These findings demonstrate that social behavior in males over the lifespan are regulated by microglia-specific mechanisms that are shaped by events that occur in early development.
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Affiliation(s)
- Evan A Bordt
- Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital for Children, Harvard Medical School, Boston, MA 02129, USA
| | - Haley A Moya
- Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital for Children, Harvard Medical School, Boston, MA 02129, USA
| | - Young Chan Jo
- Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital for Children, Harvard Medical School, Boston, MA 02129, USA; Department of Psychology and Neuroscience, Duke University, Durham, NC 27708, USA
| | - Caitlin T Ravichandran
- Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital for Children, Harvard Medical School, Boston, MA 02129, USA; McLean Hospital, Belmont, MA 02478, USA
| | - Izabella M Bankowski
- Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital for Children, Harvard Medical School, Boston, MA 02129, USA
| | - Alexis M Ceasrine
- Department of Psychology and Neuroscience, Duke University, Durham, NC 27708, USA
| | - Christopher J McDougle
- Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital for Children, Harvard Medical School, Boston, MA 02129, USA; Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA
| | | | - Staci D Bilbo
- Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital for Children, Harvard Medical School, Boston, MA 02129, USA; Department of Psychology and Neuroscience, Duke University, Durham, NC 27708, USA.
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36
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Yu KKH, Basu S, Baquer G, Ahn R, Gantchev J, Jindal S, Regan MS, Abou-Mrad Z, Prabhu MC, Williams MJ, D'Souza AD, Malinowski SW, Hopland K, Elhanati Y, Stopka SA, Stortchevoi A, He Z, Sun J, Chen Y, Espejo AB, Chow KH, Yerrum S, Kao PL, Kerrigan BP, Norberg L, Nielsen D, Puduvalli VK, Huse J, Beroukhim R, Kim YSB, Goswami S, Boire A, Frisken S, Cima MJ, Holdhoff M, Lucas CHG, Bettegowda C, Levine SS, Bale TA, Brennan C, Reardon DA, Lang FF, Antonio Chiocca E, Ligon KL, White FM, Sharma P, Tabar V, Agar NYR. Investigative needle core biopsies for multi-omics in Glioblastoma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.29.23300541. [PMID: 38234840 PMCID: PMC10793534 DOI: 10.1101/2023.12.29.23300541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Glioblastoma (GBM) is a primary brain cancer with an abysmal prognosis and few effective therapies. The ability to investigate the tumor microenvironment before and during treatment would greatly enhance both understanding of disease response and progression, as well as the delivery and impact of therapeutics. Stereotactic biopsies are a routine surgical procedure performed primarily for diagnostic histopathologic purposes. The role of investigative biopsies - tissue sampling for the purpose of understanding tumor microenvironmental responses to treatment using integrated multi-modal molecular analyses ('Multi-omics") has yet to be defined. Secondly, it is unknown whether comparatively small tissue samples from brain biopsies can yield sufficient information with such methods. Here we adapt stereotactic needle core biopsy tissue in two separate patients. In the first patient with recurrent GBM we performed highly resolved multi-omics analysis methods including single cell RNA sequencing, spatial-transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics from biopsy tissue that was obtained from a single procedure. In a second patient we analyzed multi-regional core biopsies to decipher spatial and genomic variance. We also investigated the utility of stereotactic biopsies as a method for generating patient derived xenograft models in a separate patient cohort. Dataset integration across modalities showed good correspondence between spatial modalities, highlighted immune cell associated metabolic pathways and revealed poor correlation between RNA expression and the tumor MHC Class I immunopeptidome. In conclusion, stereotactic needle biopsy cores are of sufficient quality to generate multi-omics data, provide data rich insight into a patient's disease process and tumor immune microenvironment and can be of value in evaluating treatment responses. One sentence summary Integrative multi-omics analysis of stereotactic needle core biopsies in glioblastoma.
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Andriamboavonjy L, MacDonald A, Hamilton LK, Labrecque M, Boivin MN, Karamchandani J, Stratton JA, Tetreault M. Comparative analysis of methods to reduce activation signature gene expression in PBMCs. Sci Rep 2023; 13:23086. [PMID: 38155174 PMCID: PMC10754832 DOI: 10.1038/s41598-023-49611-2] [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: 07/14/2023] [Accepted: 12/10/2023] [Indexed: 12/30/2023] Open
Abstract
Preserving the in vivo cell transcriptome is essential for accurate profiling, yet factors during cell isolation including time ex vivo and temperature induce artifactual gene expression, particularly in stress-responsive immune cells. In this study, we investigated two methods to mitigate ex vivo activation signature gene (ASG) expression in peripheral blood mononuclear cells (PBMCs): transcription and translation inhibitors (TTis) and cold temperatures during isolation. Comparative analysis of PBMCs isolated with TTis revealed reduced ASG expression. However, TTi treatment impaired responsiveness to LPS stimulation in subsequent in vitro experiments. In contrast, cold isolation methods also prevented ASG expression; up to a point where the addition of TTis during cold isolation offered minimal additional advantage. These findings highlight the importance of considering the advantages and drawbacks of different isolation methods to ensure accurate interpretation of PBMC transcriptomic profiles.
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Affiliation(s)
- Lovatiana Andriamboavonjy
- Research Center of the University of Montreal Hospital (CRCHUM), Université de Montréal, Montreal, Canada
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Adam MacDonald
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Canada
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Laura K Hamilton
- Research Center of the University of Montreal Hospital (CRCHUM), Université de Montréal, Montreal, Canada
| | - Marjorie Labrecque
- Research Center of the University of Montreal Hospital (CRCHUM), Université de Montréal, Montreal, Canada
| | - Marie-Noёlle Boivin
- C-BIG Repository (C-BIG), Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Jason Karamchandani
- C-BIG Repository (C-BIG), Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
- Department of Pathology, Montreal Neurological Institute, Montreal, QC, Canada
| | - Jo Anne Stratton
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Canada.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
| | - Martine Tetreault
- Research Center of the University of Montreal Hospital (CRCHUM), Université de Montréal, Montreal, Canada.
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montreal, Canada.
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38
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Eskandar S, Bezemer RE, Eggen BJL, Prins JR. Cold Mechanical Isolation of Placental Macrophages as a Method to Limit Procedure-Induced Activation of Macrophages. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1868-1876. [PMID: 37909834 PMCID: PMC10694029 DOI: 10.4049/jimmunol.2300379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/15/2023] [Indexed: 11/03/2023]
Abstract
Isolation of placental macrophages using enzymatic digestion at warm temperatures is widely used for in vitro studies. However, studies in brain and kidney tissue show that this method activates immune cells, immediate early genes, and heat shock proteins. Isolating placental macrophages while preserving their tissue-specific characteristics as much as possible is pivotal to reliably studying their functions. We therefore developed a mechanical dissociation protocol at low temperatures and compared this to enzymatic digestion at high temperatures. Decidual and villous macrophages were isolated from term human placentas. A cell suspension was generated by mechanical dissociation using a gentleMACS. For warm enzymatic digestion, Accutase was added, followed by incubation at 37°C. Macrophages were isolated after Ficoll density gradient centrifugation. Cell types were analyzed with flow cytometry (CD45, CD14, CD80, CD86, CD163, and CD206) and their activation status with real-time PCR (FOS, JUN, HSP27, HSP70, IL1β, TNFα, IL10, and TGFβ) after cell sorting. A higher proportion of leukocytes and macrophages was obtained from the villi with cold mechanical dissociation (p < 0.05). Compared to warm enzymatic digestion, cold mechanical dissociation resulted in a higher expression of CD163 in villous and decidual macrophages (p < 0.05). Warm enzymatic digestion showed higher levels of TNFα, IL1β, and IL10 in decidual and villous macrophages, and HSP70 in villous macrophages. Our data show that mechanical dissociation of placental tissue at low temperatures is associated with less activation of placental macrophages. This suggests that cold mechanical dissociation is a preferred method, resulting in macrophages that more closely resemble their in-tissue state.
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Affiliation(s)
- Sharon Eskandar
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Romy E. Bezemer
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bart J. L. Eggen
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jelmer R. Prins
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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Barclay KM, Abduljawad N, Cheng Z, Kim MW, Zhou L, Yang J, Rustenhoven J, Perez JM, Smyth L, Beatty W, Hou J, Saligrama N, Colonna M, Yu G, Kipnis J, Li Q. An inducible genetic tool for tracking and manipulating specific microglial states in development and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569597. [PMID: 38106187 PMCID: PMC10723357 DOI: 10.1101/2023.12.01.569597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Recent single-cell RNA sequencing studies have revealed distinct microglial states in development and disease. These include proliferative region-associated microglia (PAM) in developing white matter and disease-associated microglia (DAM) prevalent in various neurodegenerative conditions. PAM and DAM share a similar core gene signature and other functional properties. However, the extent of the dynamism and plasticity of these microglial states, as well as their functional significance, remains elusive, partly due to the lack of specific tools. Here, we report the generation of an inducible Cre driver line, Clec7a-CreERT2, designed to target PAM and DAM in the brain parenchyma. Utilizing this tool, we profile labeled cells during development and in several disease models, uncovering convergence and context-dependent differences in PAM/DAM gene expression. Through long-term tracking, we demonstrate surprising levels of plasticity in these microglial states. Lastly, we specifically depleted DAM in cuprizone-induced demyelination, revealing their roles in disease progression and recovery.
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Affiliation(s)
- Kia M. Barclay
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Neuroscience Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nora Abduljawad
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Neuroscience Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Zuolin Cheng
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Min Woo Kim
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Immunology Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lu Zhou
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jin Yang
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Justin Rustenhoven
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Jose Mazzitelli Perez
- Neuroscience Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Leon Smyth
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Wandy Beatty
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - JinChao Hou
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Naresha Saligrama
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Department of Neurology, Washington University School of Medicine in St. Louis, School of Medicine, St. Louis, MO 63110, USA
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine in St. Louis, St. Louis, MO 63112, USA
| | - Marco Colonna
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Guoqiang Yu
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Jonathan Kipnis
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Qingyun Li
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, School of Medicine, St. Louis, MO 63110, USA
- Lead Contact
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40
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Yeoh WJ, Krebs P. SHIP1 and its role for innate immune regulation-Novel targets for immunotherapy. Eur J Immunol 2023; 53:e2350446. [PMID: 37742135 DOI: 10.1002/eji.202350446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/03/2023] [Accepted: 09/21/2023] [Indexed: 09/25/2023]
Abstract
Phosphoinositide-3-kinase/AKT (PI3K/AKT) signaling plays key roles in the regulation of cellular activity in both health and disease. In immune cells, this PI3K/AKT pathway is critically regulated by the phosphoinositide phosphatase SHIP1, which has been reported to modulate the function of most immune subsets. In this review, we summarize our current knowledge of SHIP1 with a focus on innate immune cells, where we reflect on the most pertinent aspects described in the current literature. We also present several small-molecule agonists and antagonists of SHIP1 developed over the last two decades, which have led to improved outcomes in several preclinical models of disease. We outline these promising findings and put them in relation to human diseases with unmet medical needs, where we discuss the most attractive targets for immune therapies based on SHIP1 modulation.
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Affiliation(s)
- Wen Jie Yeoh
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Philippe Krebs
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
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41
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Langlieb J, Sachdev NS, Balderrama KS, Nadaf NM, Raj M, Murray E, Webber JT, Vanderburg C, Gazestani V, Tward D, Mezias C, Li X, Flowers K, Cable DM, Norton T, Mitra P, Chen F, Macosko EZ. The molecular cytoarchitecture of the adult mouse brain. Nature 2023; 624:333-342. [PMID: 38092915 PMCID: PMC10719111 DOI: 10.1038/s41586-023-06818-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
The function of the mammalian brain relies upon the specification and spatial positioning of diversely specialized cell types. Yet, the molecular identities of the cell types and their positions within individual anatomical structures remain incompletely known. To construct a comprehensive atlas of cell types in each brain structure, we paired high-throughput single-nucleus RNA sequencing with Slide-seq1,2-a recently developed spatial transcriptomics method with near-cellular resolution-across the entire mouse brain. Integration of these datasets revealed the cell type composition of each neuroanatomical structure. Cell type diversity was found to be remarkably high in the midbrain, hindbrain and hypothalamus, with most clusters requiring a combination of at least three discrete gene expression markers to uniquely define them. Using these data, we developed a framework for genetically accessing each cell type, comprehensively characterized neuropeptide and neurotransmitter signalling, elucidated region-specific specializations in activity-regulated gene expression and ascertained the heritability enrichment of neurological and psychiatric phenotypes. These data, available as an online resource ( www.BrainCellData.org ), should find diverse applications across neuroscience, including the construction of new genetic tools and the prioritization of specific cell types and circuits in the study of brain diseases.
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Affiliation(s)
| | | | | | - Naeem M Nadaf
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mukund Raj
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | | | - Daniel Tward
- Departments of Computational Medicine and Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chris Mezias
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xu Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Dylan M Cable
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Partha Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard Stem Cell and Regenerative Biology, Cambridge, MA, USA.
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
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42
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Kuhrt LD, Motta E, Elmadany N, Weidling H, Fritsche-Guenther R, Efe IE, Cobb O, Chatterjee J, Boggs LG, Schnauß M, Diecke S, Semtner M, Anastasaki C, Gutmann DH, Kettenmann H. Neurofibromin 1 mutations impair the function of human induced pluripotent stem cell-derived microglia. Dis Model Mech 2023; 16:dmm049861. [PMID: 37990867 PMCID: PMC10740172 DOI: 10.1242/dmm.049861] [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: 09/01/2022] [Accepted: 11/10/2023] [Indexed: 11/23/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant condition caused by germline mutations in the neurofibromin 1 (NF1) gene. Children with NF1 are prone to the development of multiple nervous system abnormalities, including autism and brain tumors, which could reflect the effect of NF1 mutation on microglia function. Using heterozygous Nf1-mutant mice, we previously demonstrated that impaired purinergic signaling underlies deficits in microglia process extension and phagocytosis in situ. To determine whether these abnormalities are also observed in human microglia in the setting of NF1, we leveraged an engineered isogenic series of human induced pluripotent stem cells to generate human microglia-like (hiMGL) cells heterozygous for three different NF1 gene mutations found in patients with NF1. Whereas all NF1-mutant and isogenic control hiMGL cells expressed classical microglia markers and exhibited similar transcriptomes and cytokine/chemokine release profiles, only NF1-mutant hiMGL cells had defects in P2X receptor activation, phagocytosis and motility. Taken together, these findings indicate that heterozygous NF1 mutations impair a subset of the functional properties of human microglia, which could contribute to the neurological abnormalities seen in children with NF1.
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Affiliation(s)
- Leonard D. Kuhrt
- Cellular Neurosciences, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Technology Platform Pluripotent Stem Cells, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Edyta Motta
- Cellular Neurosciences, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Department of Neurosurgery, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Nirmeen Elmadany
- Cellular Neurosciences, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- German Cancer Consortium (DKTK), Clinical Cooperation Unit (CCU), Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim (MCTN), University of Heidelberg, 68167 Mannheim, Germany
| | - Hannah Weidling
- Cellular Neurosciences, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Raphaela Fritsche-Guenther
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, BIH Metabolomics Platform, 13353 Berlin, Germany
| | - Ibrahim E. Efe
- Cellular Neurosciences, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Olivia Cobb
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jit Chatterjee
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lucy G. Boggs
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marina Schnauß
- Cellular Neurosciences, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Sebastian Diecke
- Technology Platform Pluripotent Stem Cells, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Marcus Semtner
- Cellular Neurosciences, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Klinik für Augenheilkunde, Charité – Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Corina Anastasaki
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David H. Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Helmut Kettenmann
- Cellular Neurosciences, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China, 518000
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43
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Evans KT, Blake K, Longworth A, Coburn MA, Insua-Rodríguez J, McMullen TP, Nguyen QH, Ma D, Lev T, Hernandez GA, Oganyan AK, Orujyan D, Edwards RA, Pridans C, Green KN, Villalta SA, Blurton-Jones M, Lawson DA. Microglia promote anti-tumour immunity and suppress breast cancer brain metastasis. Nat Cell Biol 2023; 25:1848-1859. [PMID: 37957324 DOI: 10.1038/s41556-023-01273-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: 04/08/2021] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Breast cancer brain metastasis (BCBM) is a lethal disease with no effective treatments. Prior work has shown that brain cancers and metastases are densely infiltrated with anti-inflammatory, protumourigenic tumour-associated macrophages, but the role of brain-resident microglia remains controversial because they are challenging to discriminate from other tumour-associated macrophages. Using single-cell RNA sequencing, genetic and humanized mouse models, we specifically identify microglia and find that they play a distinct pro-inflammatory and tumour-suppressive role in BCBM. Animals lacking microglia show increased metastasis, decreased survival and reduced natural killer and T cell responses, showing that microglia are critical to promote anti-tumour immunity to suppress BCBM. We find that the pro-inflammatory response is conserved in human microglia, and markers of their response are associated with better prognosis in patients with BCBM. These findings establish an important role for microglia in anti-tumour immunity and highlight them as a potential immunotherapy target for brain metastasis.
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Affiliation(s)
- Katrina T Evans
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Kerrigan Blake
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - Aaron Longworth
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Morgan A Coburn
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
| | - Jacob Insua-Rodríguez
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Timothy P McMullen
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Quy H Nguyen
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Dennis Ma
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Tatyana Lev
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - Grace A Hernandez
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Armani K Oganyan
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Davit Orujyan
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Robert A Edwards
- Department of Pathology, University of California, Irvine, Irvine, CA, USA
| | - Clare Pridans
- University of Edinburgh Centre for Inflammation Research, Edinburgh, UK
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Kim N Green
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
| | - S Armando Villalta
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
| | - Devon A Lawson
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA.
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA.
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44
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Vecchiarelli HA, Tremblay MÈ. Microglial Transcriptional Signatures in the Central Nervous System: Toward A Future of Unraveling Their Function in Health and Disease. Annu Rev Genet 2023; 57:65-86. [PMID: 37384734 DOI: 10.1146/annurev-genet-022223-093643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Microglia, the resident immune cells of the central nervous system (CNS), are primarily derived from the embryonic yolk sac and make their way to the CNS during early development. They play key physiological and immunological roles across the life span, throughout health, injury, and disease. Recent transcriptomic studies have identified gene transcript signatures expressed by microglia that may provide the foundation for unprecedented insights into their functions. Microglial gene expression signatures can help distinguish them from macrophage cell types to a reasonable degree of certainty, depending on the context. Microglial expression patterns further suggest a heterogeneous population comprised of many states that vary according to the spatiotemporal context. Microglial diversity is most pronounced during development, when extensive CNS remodeling takes place, and following disease or injury. A next step of importance for the field will be to identify the functional roles performed by these various microglial states, with the perspective of targeting them therapeutically.
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Affiliation(s)
- Haley A Vecchiarelli
- Division of Medical Sciences, University of Victoria, British Columbia, Canada; ,
| | - Marie-Ève Tremblay
- Division of Medical Sciences, University of Victoria, British Columbia, Canada; ,
- Centre for Advanced Materials and Related Technology and Institute on Aging and Lifelong Health, University of Victoria, British Columbia, Canada
- Département de Médecine Moléculaire and Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Quebec, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine and Health Sciences, McGill University, Quebec, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, British Columbia, Canada
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45
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Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Hoolehan W, Kulpa AM, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. Epigenetics Chromatin 2023; 16:45. [PMID: 37953264 PMCID: PMC10642035 DOI: 10.1186/s13072-023-00522-6] [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: 06/03/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Cellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation, DNA modifications in particular, of gene expression between neurons and glia. RESULTS After validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT-whole genome oxidative bisulfite sequencing (WGoxBS) to assess the neuronal translatome and epigenome in the hippocampus of young mice (4 months old). WGoxBS findings were validated with enzymatic methyl-Seq (EM-Seq) and nanopore sequencing. Comparing neuronal data to microglial and astrocytic data from NuTRAP models, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, rather than proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of gene body mCG and a positive relationship between distal promoter and gene body hmCG with gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions. CONCLUSIONS Neurons, astrocytes, and microglia demonstrate different genome-wide levels of mCG, hmCG, and mCH that are reproducible across analytical methods. However, modification-gene expression relationships are conserved across cell types. Enrichment of differential modifications across cell types in gene bodies and distal regulatory elements, but not proximal promoters, highlights epigenomic patterning in these regions as potentially greater determinants of cell identity. These findings also demonstrate the importance of differentiating between mC and hmC in neuroepigenomic analyses, as up to 30% of what is conventionally interpreted as mCG can be hmCG, which often has a different relationship to gene expression than mCG.
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Affiliation(s)
- Kyla B Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Ana J Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Sarah R Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adeline H Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Kevin D Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Walker Hoolehan
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adam M Kulpa
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - David R Stanford
- Center for Biomedical Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Willard M Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
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46
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Ament SA, Cortes-Gutierrez M, Herb BR, Mocci E, Colantuoni C, McCarthy MM. A single-cell genomic atlas for maturation of the human cerebellum during early childhood. Sci Transl Med 2023; 15:eade1283. [PMID: 37824600 DOI: 10.1126/scitranslmed.ade1283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/05/2023] [Indexed: 10/14/2023]
Abstract
Inflammation early in life is a clinically established risk factor for autism spectrum disorders and schizophrenia, yet the impact of inflammation on human brain development is poorly understood. The cerebellum undergoes protracted postnatal maturation, making it especially susceptible to perturbations contributing to the risk of developing neurodevelopmental disorders. Here, using single-cell genomics of postmortem cerebellar brain samples, we characterized the postnatal development of cerebellar neurons and glia in 1- to 5-year-old children, comparing individuals who had died while experiencing inflammation with those who had died as a result of an accident. Our analyses revealed that inflammation and postnatal cerebellar maturation are associated with extensive, overlapping transcriptional changes primarily in two subtypes of inhibitory neurons: Purkinje neurons and Golgi neurons. Immunohistochemical analysis of a subset of these postmortem cerebellar samples revealed no change to Purkinje neuron soma size but evidence for increased activation of microglia in those children who had experienced inflammation. Maturation-associated and inflammation-associated gene expression changes included genes implicated in neurodevelopmental disorders. A gene regulatory network model integrating cell type-specific gene expression and chromatin accessibility identified seven temporally specific gene networks in Purkinje neurons and suggested that inflammation may be associated with the premature down-regulation of developmental gene expression programs.
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Affiliation(s)
- Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
- UM-MIND, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marcia Cortes-Gutierrez
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Brian R Herb
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Evelina Mocci
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Pain Sciences, University of Maryland School of Nursing, Baltimore, MD, USA
| | - Carlo Colantuoni
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Departments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Margaret M McCarthy
- UM-MIND, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
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47
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Faigle W, Piccirelli M, Hortobágyi T, Frontzek K, Cannon AE, Zürrer WE, Granberg T, Kulcsar Z, Ludersdorfer T, Frauenknecht KBM, Reimann R, Ineichen BV. The Brainbox -a tool to facilitate correlation of brain magnetic resonance imaging features to histopathology. Brain Commun 2023; 5:fcad307. [PMID: 38025281 PMCID: PMC10664401 DOI: 10.1093/braincomms/fcad307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/20/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
Magnetic resonance imaging (MRI) has limitations in identifying underlying tissue pathology, which is relevant for neurological diseases such as multiple sclerosis, stroke or brain tumours. However, there are no standardized methods for correlating MRI features with histopathology. Thus, here we aimed to develop and validate a tool that can facilitate the correlation of brain MRI features to corresponding histopathology. For this, we designed the Brainbox, a waterproof and MRI-compatible 3D printed container with an integrated 3D coordinate system. We used the Brainbox to acquire post-mortem ex vivo MRI of eight human brains, fresh and formalin-fixed, and correlated focal imaging features to histopathology using the built-in 3D coordinate system. With its built-in 3D coordinate system, the Brainbox allowed correlation of MRI features to corresponding tissue substrates. The Brainbox was used to correlate different MR image features of interest to the respective tissue substrate, including normal anatomical structures such as the hippocampus or perivascular spaces, as well as a lacunar stroke. Brain volume decreased upon fixation by 7% (P = 0.01). The Brainbox enabled degassing of specimens before scanning, reducing susceptibility artefacts and minimizing bulk motion during scanning. In conclusion, our proof-of-principle experiments demonstrate the usability of the Brainbox, which can contribute to improving the specificity of MRI and the standardization of the correlation between post-mortem ex vivo human brain MRI and histopathology. Brainboxes are available upon request from our institution.
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Affiliation(s)
- Wolfgang Faigle
- Neuroimmunology and MS Research Section, Neurology Clinic, University Zurich, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Marco Piccirelli
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, CH-8091 Zurich, Switzerland
| | - Tibor Hortobágyi
- Institute of Neuropathology, University of Zurich, CH-8091 Zurich, Switzerland
| | - Karl Frontzek
- Institute of Neuropathology, University of Zurich, CH-8091 Zurich, Switzerland
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, WC1N 1PJ London, United Kingdom
| | - Amelia Elaine Cannon
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, CH-8091 Zurich, Switzerland
| | - Wolfgang Emanuel Zürrer
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, CH-8091 Zurich, Switzerland
| | - Tobias Granberg
- Department of Neuroradiology, Karolinska University Hospital, S-141 86 Stockholm, Sweden
| | - Zsolt Kulcsar
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, CH-8091 Zurich, Switzerland
| | - Thomas Ludersdorfer
- Neuroimmunology and MS Research Section, Neurology Clinic, University Zurich, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Katrin B M Frauenknecht
- Institute of Neuropathology, University of Zurich, CH-8091 Zurich, Switzerland
- Luxembourg Center of Neuropathology (LCNP), Laboratoire National de Santé, 3555 Dudelange, Luxembourg
- National Center of Pathology (NCP), Laboratoire National de Santé, 3555 Dudelange, Luxembourg
| | - Regina Reimann
- Institute of Neuropathology, University of Zurich, CH-8091 Zurich, Switzerland
| | - Benjamin Victor Ineichen
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, CH-8091 Zurich, Switzerland
- Center for Reproducible Science, University of Zurich, CH-8001 Zurich, Switzerland
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48
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Groh J, Abdelwahab T, Kattimani Y, Hörner M, Loserth S, Gudi V, Adalbert R, Imdahl F, Saliba AE, Coleman M, Stangel M, Simons M, Martini R. Microglia-mediated demyelination protects against CD8 + T cell-driven axon degeneration in mice carrying PLP defects. Nat Commun 2023; 14:6911. [PMID: 37903797 PMCID: PMC10616105 DOI: 10.1038/s41467-023-42570-2] [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: 01/27/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
Axon degeneration and functional decline in myelin diseases are often attributed to loss of myelin but their relation is not fully understood. Perturbed myelinating glia can instigate chronic neuroinflammation and contribute to demyelination and axonal damage. Here we study mice with distinct defects in the proteolipid protein 1 gene that develop axonal damage which is driven by cytotoxic T cells targeting myelinating oligodendrocytes. We show that persistent ensheathment with perturbed myelin poses a risk for axon degeneration, neuron loss, and behavioral decline. We demonstrate that CD8+ T cell-driven axonal damage is less likely to progress towards degeneration when axons are efficiently demyelinated by activated microglia. Mechanistically, we show that cytotoxic T cell effector molecules induce cytoskeletal alterations within myelinating glia and aberrant actomyosin constriction of axons at paranodal domains. Our study identifies detrimental axon-glia-immune interactions which promote neurodegeneration and possible therapeutic targets for disorders associated with myelin defects and neuroinflammation.
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Affiliation(s)
- Janos Groh
- Department of Neurology, Section of Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany.
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany.
| | - Tassnim Abdelwahab
- Department of Neurology, Section of Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Yogita Kattimani
- Department of Neurology, Section of Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Michaela Hörner
- Department of Neurology, Section of Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
- Department of Neurology, Section of Neurodegeneration, University Hospital Heidelberg, Heidelberg, Germany
| | - Silke Loserth
- Department of Neurology, Section of Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Viktoria Gudi
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Robert Adalbert
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, UK
- Department of Anatomy, Histology and Embryology, University of Szeged, Szeged, Hungary
- Institute of Health Sciences Education, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Fabian Imdahl
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Michael Coleman
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, UK
| | - Martin Stangel
- Department of Neurology, Hannover Medical School, Hannover, Germany
- Translational Medicine, Novartis Institute of Biomedical Research, Basel, Switzerland
| | - Mikael Simons
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
- Munich Cluster of Systems Neurology, Munich, Germany
| | - Rudolf Martini
- Department of Neurology, Section of Developmental Neurobiology, University Hospital Würzburg, Würzburg, Germany.
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49
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Hasegawa Y, Kim J, Ursini G, Jouroukhin Y, Zhu X, Miyahara Y, Xiong F, Madireddy S, Obayashi M, Lutz B, Sawa A, Brown SP, Pletnikov MV, Kamiya A. Microglial cannabinoid receptor type 1 mediates social memory deficits in mice produced by adolescent THC exposure and 16p11.2 duplication. Nat Commun 2023; 14:6559. [PMID: 37880248 PMCID: PMC10600150 DOI: 10.1038/s41467-023-42276-5] [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: 03/13/2022] [Accepted: 10/04/2023] [Indexed: 10/27/2023] Open
Abstract
Adolescent cannabis use increases the risk for cognitive impairments and psychiatric disorders. Cannabinoid receptor type 1 (Cnr1) is expressed not only in neurons and astrocytes, but also in microglia, which shape synaptic connections during adolescence. However, the role of microglia in mediating the adverse cognitive effects of delta-9-tetrahydrocannabinol (THC), the principal psychoactive constituent of cannabis, is not fully understood. Here, we report that in mice, adolescent THC exposure produces microglial apoptosis in the medial prefrontal cortex (mPFC), which was exacerbated in a model of 16p11.2 duplication, a representative copy number variation (CNV) risk factor for psychiatric disorders. These effects are mediated by microglial Cnr1, leading to reduction in the excitability of mPFC pyramidal-tract neurons and deficits in social memory in adulthood. Our findings suggest the microglial Cnr1 may contribute to adverse effect of cannabis exposure in genetically vulnerable individuals.
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Affiliation(s)
- Yuto Hasegawa
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Juhyun Kim
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Korea Brain Research Institute, Daegu, Republic of Korea
| | - Gianluca Ursini
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Yan Jouroukhin
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences SUNY, University at Buffalo, Buffalo, NY, USA
| | - Xiaolei Zhu
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yu Miyahara
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Feiyi Xiong
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Samskruthi Madireddy
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mizuho Obayashi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Beat Lutz
- Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
- Leibniz Institute for Resilience Research (LIR) gGmbH, Mainz, Germany
| | - Akira Sawa
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Solange P Brown
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Mikhail V Pletnikov
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences SUNY, University at Buffalo, Buffalo, NY, USA.
| | - Atsushi Kamiya
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Maes ME, Colombo G, Schoot Uiterkamp FE, Sternberg F, Venturino A, Pohl EE, Siegert S. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience 2023; 26:107780. [PMID: 37731609 PMCID: PMC10507162 DOI: 10.1016/j.isci.2023.107780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/10/2023] [Accepted: 08/28/2023] [Indexed: 09/22/2023] Open
Abstract
Mitochondrial networks remodel their connectivity, content, and subcellular localization to support optimized energy production in conditions of increased environmental or cellular stress. Microglia rely on mitochondria to respond to these stressors, however our knowledge about mitochondrial networks and their adaptations in microglia in vivo is limited. Here, we generate a mouse model that selectively labels mitochondria in microglia. We identify that mitochondrial networks are more fragmented with increased content and perinuclear localization in vitro vs. in vivo. Mitochondrial networks adapt similarly in microglia closest to the injury site after optic nerve crush. Preventing microglial UCP2 increase after injury by selective knockout induces cellular stress. This results in mitochondrial hyperfusion in male microglia, a phenotype absent in females due to circulating estrogens. Our results establish the foundation for mitochondrial network analysis of microglia in vivo, emphasizing the importance of mitochondrial-based sex effects of microglia in other pathologies.
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Affiliation(s)
- Margaret E. Maes
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Gloria Colombo
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | | | - Felix Sternberg
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - Alessandro Venturino
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Elena E. Pohl
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - Sandra Siegert
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
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