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Zeng Y, Ma Q, Chen J, Kong X, Chen Z, Liu H, Liu L, Qian Y, Wang X, Lu S. Single-cell sequencing: Current applications in various tuberculosis specimen types. Cell Prolif 2024:e13698. [PMID: 38956399 DOI: 10.1111/cpr.13698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/21/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
Tuberculosis (TB) is a chronic disease caused by Mycobacterium tuberculosis (M.tb) and responsible for millions of deaths worldwide each year. It has a complex pathogenesis that primarily affects the lungs but can also impact systemic organs. In recent years, single-cell sequencing technology has been utilized to characterize the composition and proportion of immune cell subpopulations associated with the pathogenesis of TB disease since it has a high resolution that surpasses conventional techniques. This paper reviews the current use of single-cell sequencing technologies in TB research and their application in analysing specimens from various sources of TB, primarily peripheral blood and lung specimens. The focus is on how these technologies can reveal dynamic changes in immune cell subpopulations, genes and proteins during disease progression after M.tb infection. Based on the current findings, single-cell sequencing has significant potential clinical value in the field of TB research. Next, we will focus on the real-world applications of the potential targets identified through single-cell sequencing for diagnostics, therapeutics and the development of effective vaccines.
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Affiliation(s)
- Yuqin Zeng
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Quan Ma
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Jinyun Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xingxing Kong
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Zhanpeng Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Huazhen Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Lanlan Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Yan Qian
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xiaomin Wang
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Shuihua Lu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
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2
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Ravindran A, Holappa L, Niskanen H, Skovorodkin I, Kaisto S, Beter M, Kiema M, Selvarajan I, Nurminen V, Aavik E, Aherrahrou R, Pasonen-Seppänen S, Fortino V, Laakkonen JP, Ylä-Herttuala S, Vainio S, Örd T, Kaikkonen MU. Translatome profiling reveals Itih4 as a novel smooth muscle cell-specific gene in atherosclerosis. Cardiovasc Res 2024; 120:869-882. [PMID: 38289873 PMCID: PMC11218691 DOI: 10.1093/cvr/cvae028] [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: 03/29/2023] [Revised: 12/01/2023] [Accepted: 12/12/2023] [Indexed: 02/01/2024] Open
Abstract
AIMS Vascular smooth muscle cells (SMCs) and their derivatives are key contributors to the development of atherosclerosis. However, studying changes in SMC gene expression in heterogeneous vascular tissues is challenging due to the technical limitations and high cost associated with current approaches. In this paper, we apply translating ribosome affinity purification sequencing to profile SMC-specific gene expression directly from tissue. METHODS AND RESULTS To facilitate SMC-specific translatome analysis, we generated SMCTRAP mice, a transgenic mouse line expressing enhanced green fluorescent protein (EGFP)-tagged ribosomal protein L10a (EGFP-L10a) under the control of the SMC-specific αSMA promoter. These mice were further crossed with the atherosclerosis model Ldlr-/-, ApoB100/100 to generate SMCTRAP-AS mice and used to profile atherosclerosis-associated SMCs in thoracic aorta samples of 15-month-old SMCTRAP and SMCTRAP-AS mice. Our analysis of SMCTRAP-AS mice showed that EGFP-L10a expression was localized to SMCs in various tissues, including the aortic wall and plaque. The TRAP fraction demonstrated high enrichment of known SMC-specific genes, confirming the specificity of our approach. We identified several genes, including Cemip, Lum, Mfge8, Spp1, and Serpina3, which are known to be involved in atherosclerosis-induced gene expression. Moreover, we identified several novel genes not previously linked to SMCs in atherosclerosis, such as Anxa4, Cd276, inter-alpha-trypsin inhibitor-4 (Itih4), Myof, Pcdh11x, Rab31, Serpinb6b, Slc35e4, Slc8a3, and Spink5. Among them, we confirmed the SMC-specific expression of Itih4 in atherosclerotic lesions using immunofluorescence staining of mouse aortic roots and spatial transcriptomics of human carotid arteries. Furthermore, our more detailed analysis of Itih4 showed its link to coronary artery disease through the colocalization of genome-wide association studies, splice quantitative trait loci (QTL), and protein QTL signals. CONCLUSION We generated a SMC-specific TRAP mouse line to study atherosclerosis and identified Itih4 as a novel SMC-expressed gene in atherosclerotic plaques, warranting further investigation of its putative function in extracellular matrix stability and genetic evidence of causality.
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MESH Headings
- Animals
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Atherosclerosis/genetics
- Atherosclerosis/metabolism
- Atherosclerosis/pathology
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Disease Models, Animal
- Aortic Diseases/genetics
- Aortic Diseases/pathology
- Aortic Diseases/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Plaque, Atherosclerotic
- Mice, Inbred C57BL
- Male
- Gene Expression Regulation
- Gene Expression Profiling
- Phenotype
- Transcriptome
- Receptors, LDL/genetics
- Receptors, LDL/metabolism
- Apolipoprotein B-100/genetics
- Apolipoprotein B-100/metabolism
- Mice, Knockout
- Humans
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- Mice
- Mice, Transgenic
- Aorta/metabolism
- Aorta/pathology
- Female
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Affiliation(s)
- Aarthi Ravindran
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Lari Holappa
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Henri Niskanen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Ilya Skovorodkin
- Disease networks research unit, Faculty of Biochemistry and Molecular Medicine, Kvantum Institute, Infotech Oulu, University of Oulu, Oulu, Finland
| | - Susanna Kaisto
- Disease networks research unit, Faculty of Biochemistry and Molecular Medicine, Kvantum Institute, Infotech Oulu, University of Oulu, Oulu, Finland
| | - Mustafa Beter
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Miika Kiema
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Ilakya Selvarajan
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Valtteri Nurminen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Einari Aavik
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Rédouane Aherrahrou
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
- Institute for Cardiogenetics, Universität zu Lübeck, 23562 Lübeck, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, University Heart Centre Lübeck, 23562 Lübeck, Germany
| | - Sanna Pasonen-Seppänen
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Johanna P Laakkonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Seppo Vainio
- Disease networks research unit, Faculty of Biochemistry and Molecular Medicine, Kvantum Institute, Infotech Oulu, University of Oulu, Oulu, Finland
| | - Tiit Örd
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Minna U Kaikkonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
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3
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Lister KC, Wong C, Uttam S, Parisien M, Stecum P, Brown N, Cai W, Hooshmandi M, Gu N, Amiri M, Beaudry F, Jafarnejad SM, Tavares-Ferreira D, Inturi NN, Mazhar K, Zhao HT, Fitzsimmons B, Gkogkas CG, Sonenberg N, Price TJ, Diatchenko L, Atlasi Y, Mogil JS, Khoutorsky A. Translational control in the spinal cord regulates gene expression and pain hypersensitivity in the chronic phase of neuropathic pain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600539. [PMID: 38979173 PMCID: PMC11230214 DOI: 10.1101/2024.06.24.600539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Sensitization of spinal nociceptive circuits plays a crucial role in neuropathic pain. This sensitization depends on new gene expression that is primarily regulated via transcriptional and translational control mechanisms. The relative roles of these mechanisms in regulating gene expression in the clinically relevant chronic phase of neuropathic pain are not well understood. Here, we show that changes in gene expression in the spinal cord during the chronic phase of neuropathic pain are substantially regulated at the translational level. Downregulating spinal translation at the chronic phase alleviated pain hypersensitivity. Cell-type-specific profiling revealed that spinal inhibitory neurons exhibited greater changes in translation after peripheral nerve injury compared to excitatory neurons. Notably, increasing translation selectively in all inhibitory neurons or parvalbumin-positive (PV + ) interneurons, but not excitatory neurons, promoted mechanical pain hypersensitivity. Furthermore, increasing translation in PV + neurons decreased their intrinsic excitability and spiking activity, whereas reducing translation in spinal PV + neurons prevented the nerve injury-induced decrease in excitability. Thus, translational control mechanisms in the spinal cord, particularly in inhibitory neurons, play a role in mediating neuropathic pain hypersensitivity.
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4
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O'Shea TM, Ao Y, Wang S, Ren Y, Cheng AL, Kawaguchi R, Shi Z, Swarup V, Sofroniew MV. Derivation and transcriptional reprogramming of border-forming wound repair astrocytes after spinal cord injury or stroke in mice. Nat Neurosci 2024:10.1038/s41593-024-01684-6. [PMID: 38907165 DOI: 10.1038/s41593-024-01684-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 05/15/2024] [Indexed: 06/23/2024]
Abstract
Central nervous system (CNS) lesions become surrounded by neuroprotective borders of newly proliferated reactive astrocytes; however, fundamental features of these cells are poorly understood. Here we show that following spinal cord injury or stroke, 90% and 10% of border-forming astrocytes derive, respectively, from proliferating local astrocytes and oligodendrocyte progenitor cells in adult mice of both sexes. Temporal transcriptome analysis, single-nucleus RNA sequencing and immunohistochemistry show that after focal CNS injury, local mature astrocytes dedifferentiate, proliferate and become transcriptionally reprogrammed to permanently altered new states, with persisting downregulation of molecules associated with astrocyte-neuron interactions and upregulation of molecules associated with wound healing, microbial defense and interactions with stromal and immune cells. These wound repair astrocytes share morphologic and transcriptional features with perimeningeal limitans astrocytes and are the predominant source of neuroprotective borders that re-establish CNS integrity around lesions by separating neural parenchyma from stromal and immune cells as occurs throughout the healthy CNS.
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Affiliation(s)
- Timothy M O'Shea
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
| | - Yan Ao
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Shinong Wang
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Yilong Ren
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, PR China
| | - Amy L Cheng
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Riki Kawaguchi
- Departments of Psychiatry and Neurology, University of California Los Angeles, Los Angeles, CA, USA
| | - Zechuan Shi
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA, USA
| | - Michael V Sofroniew
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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5
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Matuskova H, Porschen LT, Matthes F, Lindgren AG, Petzold GC, Meissner A. Spatiotemporal sphingosine-1-phosphate receptor 3 expression within the cerebral vasculature after ischemic stroke. iScience 2024; 27:110031. [PMID: 38868192 PMCID: PMC11167442 DOI: 10.1016/j.isci.2024.110031] [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: 11/01/2023] [Revised: 03/29/2024] [Accepted: 05/16/2024] [Indexed: 06/14/2024] Open
Abstract
Sphingosine-1-phosphate receptors (S1PRs) are promising therapeutic targets in cardiovascular disease, including ischemic stroke. However, important spatiotemporal information for alterations of S1PR expression is lacking. Here, we investigated the role of S1PR3 in ischemic stroke in rodent models and patient samples. We show that S1PR3 is acutely upregulated in perilesional reactive astrocytes after stroke, and that stroke volume and behavioral deficits are improved in mice lacking S1PR3. Further, we find that administration of an S1PR3 antagonist at 4-h post-stroke, but not at later timepoints, improves stroke outcome. Lastly, we observed higher plasma S1PR3 concentrations in experimental stroke and in patients with ischemic stroke. Together, our results establish S1PR3 as a potential drug target and biomarker in ischemic stroke.
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Affiliation(s)
- Hana Matuskova
- Department of Experimental Medical Sciences, Lund University, 221 84 Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, 221 84 Lund, Sweden
- Division of Vascular Neurology, University Hospital Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Lisa T. Porschen
- Department of Experimental Medical Sciences, Lund University, 221 84 Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, 221 84 Lund, Sweden
- Department of Physiology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Frank Matthes
- Department of Experimental Medical Sciences, Lund University, 221 84 Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, 221 84 Lund, Sweden
- Department of Physiology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Arne G. Lindgren
- Department of Clinical Sciences Lund, Neurology, Lund University, Lund, Sweden
- Department of Neurology, Rehabilitation Medicine, Memory Disorders and Geriatrics, Skåne University Hospital, Lund, Sweden
| | - Gabor C. Petzold
- Division of Vascular Neurology, University Hospital Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Anja Meissner
- Department of Experimental Medical Sciences, Lund University, 221 84 Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, 221 84 Lund, Sweden
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
- Department of Physiology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
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6
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Huang M, Pieraut S, Cao J, de Souza Polli F, Roncace V, Shen G, Ramos-Medina C, Lee H, Maximov A. Nr4a1 regulates cell-specific transcriptional programs in inhibitory GABAergic interneurons. Neuron 2024; 112:2031-2044.e7. [PMID: 38754414 PMCID: PMC11189749 DOI: 10.1016/j.neuron.2024.03.018] [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: 01/12/2023] [Revised: 01/29/2024] [Accepted: 03/14/2024] [Indexed: 05/18/2024]
Abstract
The patterns of synaptic connectivity and physiological properties of diverse neuron types are shaped by distinct gene sets. Our study demonstrates that, in the mouse forebrain, the transcriptional profiles of inhibitory GABAergic interneurons are regulated by Nr4a1, an orphan nuclear receptor whose expression is transiently induced by sensory experiences and is required for normal learning. Nr4a1 exerts contrasting effects on the local axonal wiring of parvalbumin- and somatostatin-positive interneurons, which innervate different subcellular domains of their postsynaptic partners. The loss of Nr4a1 activity in these interneurons results in bidirectional, cell-type-specific transcriptional switches across multiple gene families, including those involved in surface adhesion and repulsion. Our findings reveal that combinatorial synaptic organizing codes are surprisingly flexible and highlight a mechanism by which inducible transcription factors can influence neural circuit structure and function.
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Affiliation(s)
- Min Huang
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA; The Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Simon Pieraut
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jasmine Cao
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Filip de Souza Polli
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Vincenzo Roncace
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gloria Shen
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Carlos Ramos-Medina
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - HeeYang Lee
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA; The Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anton Maximov
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA.
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7
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Paudel S, Lee N. Epstein-Barr virus noncoding RNA EBER1 promotes the expression of a ribosomal protein paralog to boost oxidative phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.15.599158. [PMID: 38915488 PMCID: PMC11195164 DOI: 10.1101/2024.06.15.599158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Epstein-Barr virus (EBV) is a highly successful pathogen that infects ~95% of the adult population and is associated with diverse cancers and autoimmune diseases. The most abundant viral factor in latently infected cells is not a protein but a noncoding RNA called EBV-encoded RNA 1 (EBER1). Even though EBER1 is highly abundant and was discovered over forty years ago, the function of EBER1 has remained elusive. EBER1 interacts with the ribosomal protein L22, which normally suppresses the expression of its paralog L22-like 1 (L22L1). Here we show that when L22 binds EBER1, it cannot suppress L22L1, resulting in L22L1 being expressed and incorporated into ribosomes. We further show that L22L1-containing ribosomes preferentially translate mRNAs involved in the oxidative phosphorylation pathway. Moreover, upregulation of L22L1 is indispensable for growth transformation and immortalization of resting B cells upon EBV infection. Taken together, our results suggest that the function of EBER1 is to modulate host gene expression at the translational level, thus bypassing the need for dysregulating host gene transcription.
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Affiliation(s)
- Sita Paudel
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
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8
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Raza Q, Nadeem T, Youn SW, Swaminathan B, Gupta A, Sargis T, Du J, Cuervo H, Eichmann A, Ackerman SL, Naiche LA, Kitajewski J. Notch signaling regulates UNC5B to suppress endothelial proliferation, migration, junction activity, and retinal plexus branching. Sci Rep 2024; 14:13603. [PMID: 38866944 PMCID: PMC11169293 DOI: 10.1038/s41598-024-64375-z] [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: 03/21/2024] [Accepted: 06/07/2024] [Indexed: 06/14/2024] Open
Abstract
Notch signaling guides vascular development and function by regulating diverse endothelial cell behaviors, including migration, proliferation, vascular density, endothelial junctions, and polarization in response to flow. Notch proteins form transcriptional activation complexes that regulate endothelial gene expression, but few of the downstream effectors that enable these phenotypic changes have been characterized in endothelial cells, limiting our understanding of vascular Notch activities. Using an unbiased screen of translated mRNA rapidly regulated by Notch signaling, we identified novel in vivo targets of Notch signaling in neonatal mouse brain endothelium, including UNC5B, a member of the netrin family of angiogenic-regulatory receptors. Endothelial Notch signaling rapidly upregulates UNC5B in multiple endothelial cell types. Loss or gain of UNC5B recapitulated specific Notch-regulated phenotypes. UNC5B expression inhibited endothelial migration and proliferation and was required for stabilization of endothelial junctions in response to shear stress. Loss of UNC5B partially or wholly blocked the ability of Notch activation to regulate these endothelial cell behaviors. In the developing mouse retina, endothelial-specific loss of UNC5B led to excessive vascularization, including increased vascular outgrowth, density, and branchpoint count. These data indicate that Notch signaling upregulates UNC5B as an effector protein to control specific endothelial cell behaviors and inhibit angiogenic growth.
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Affiliation(s)
- Qanber Raza
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, 1853 W Polk St, Rm 522 (MC 901), Chicago, IL, 60612, USA
| | - Taliha Nadeem
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, 1853 W Polk St, Rm 522 (MC 901), Chicago, IL, 60612, USA
| | - Seock-Won Youn
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, 1853 W Polk St, Rm 522 (MC 901), Chicago, IL, 60612, USA
| | - Bhairavi Swaminathan
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, 1853 W Polk St, Rm 522 (MC 901), Chicago, IL, 60612, USA
| | - Ahana Gupta
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, 1853 W Polk St, Rm 522 (MC 901), Chicago, IL, 60612, USA
| | - Timothy Sargis
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, 1853 W Polk St, Rm 522 (MC 901), Chicago, IL, 60612, USA
| | - Jing Du
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, 1853 W Polk St, Rm 522 (MC 901), Chicago, IL, 60612, USA
| | - Henar Cuervo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III- CNIC- (F.S.P), Madrid, Spain
| | | | | | - L A Naiche
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, 1853 W Polk St, Rm 522 (MC 901), Chicago, IL, 60612, USA.
| | - Jan Kitajewski
- Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, 1853 W Polk St, Rm 522 (MC 901), Chicago, IL, 60612, USA
- University of Illinois Cancer Center, Chicago, USA
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9
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Serrano J, Boyd J, Brown IS, Mason C, Smith KR, Karolyi K, Maurya SK, Meshram NN, Serna V, Link GM, Gardell SJ, Kyriazis GA. The TAS1R2 G-protein-coupled receptor is an ambient glucose sensor in skeletal muscle that regulates NAD homeostasis and mitochondrial capacity. Nat Commun 2024; 15:4915. [PMID: 38851747 PMCID: PMC11162498 DOI: 10.1038/s41467-024-49100-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
The bioavailability of nicotinamide adenine dinucleotide (NAD) is vital for skeletal muscle health, yet the mechanisms or signals regulating NAD homeostasis remain unclear. Here, we uncover a pathway connecting peripheral glucose sensing to the modulation of muscle NAD through TAS1R2, the sugar-sensing G protein-coupled receptor (GPCR) initially identified in taste perception. Muscle TAS1R2 receptor stimulation by glucose and other agonists induces ERK1/2-dependent phosphorylation and activation of poly(ADP-ribose) polymerase1 (PARP1), a major NAD consumer in skeletal muscle. Consequently, muscle-specific deletion of TAS1R2 (mKO) in male mice suppresses PARP1 activity, elevating NAD levels and enhancing mitochondrial capacity and running endurance. Plasma glucose levels negatively correlate with muscle NAD, and TAS1R2 receptor deficiency enhances NAD responses across the glycemic range, implicating TAS1R2 as a peripheral energy surveyor. These findings underscore the role of GPCR signaling in NAD regulation and propose TAS1R2 as a potential therapeutic target for maintaining muscle health.
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Affiliation(s)
- Joan Serrano
- Biological Chemistry & Pharmacology, College of Medicine, The Ohio State University; Columbus, Columbus, 43210, USA
| | - Jordan Boyd
- Biological Chemistry & Pharmacology, College of Medicine, The Ohio State University; Columbus, Columbus, 43210, USA
| | - Ian S Brown
- Biological Chemistry & Pharmacology, College of Medicine, The Ohio State University; Columbus, Columbus, 43210, USA
| | - Carter Mason
- Biological Chemistry & Pharmacology, College of Medicine, The Ohio State University; Columbus, Columbus, 43210, USA
| | - Kathleen R Smith
- Biological Chemistry & Pharmacology, College of Medicine, The Ohio State University; Columbus, Columbus, 43210, USA
| | - Katalin Karolyi
- Biological Chemistry & Pharmacology, College of Medicine, The Ohio State University; Columbus, Columbus, 43210, USA
| | - Santosh K Maurya
- Physiology and Cell Biology, College of Medicine, The Ohio State University; Columbus, Columbus, 43210, USA
| | - Nishita N Meshram
- Biological Chemistry & Pharmacology, College of Medicine, The Ohio State University; Columbus, Columbus, 43210, USA
| | - Vanida Serna
- Biological Chemistry & Pharmacology, College of Medicine, The Ohio State University; Columbus, Columbus, 43210, USA
| | - Grace M Link
- Biological Chemistry & Pharmacology, College of Medicine, The Ohio State University; Columbus, Columbus, 43210, USA
| | - Stephen J Gardell
- Translational Research Institute, Advent Health, Orlando, 32804, USA
| | - George A Kyriazis
- Biological Chemistry & Pharmacology, College of Medicine, The Ohio State University; Columbus, Columbus, 43210, USA.
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10
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Gonzales J, Dharshika C, Mazhar K, Morales-Soto W, McClain JL, Moeser AJ, Nault R, Price TJ, Gulbransen BD. Early life adversity promotes gastrointestinal dysfunction through a sex-dependent phenotypic switch in enteric glia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596805. [PMID: 38895433 PMCID: PMC11185517 DOI: 10.1101/2024.05.31.596805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Irritable bowel syndrome and related disorders of gut-brain interaction (DGBI) are common and exhibit a complex, poorly understood etiology that manifests as abnormal gut motility and pain. Risk factors such as biological sex, stressors during critical periods, and inflammation are thought to influence DGBI vulnerability by reprogramming gut-brain circuits, but the specific cells affected are unclear. Here, we used a model of early life stress to understand cellular mechanisms in the gut that produce DGBIs. Our findings identify enteric glia as a key cellular substrate in which stress and biological sex converge to dictate DGBI susceptibility. Enteric glia exhibit sexual dimorphism in genes and functions related to cellular communication, inflammation, and disease susceptibility. Experiencing early life stress has sex-specific effects on enteric glia that cause a phenotypic switch in male glia toward a phenotype normally observed in females. This phenotypic transformation is followed by physiological changes in the gut, mirroring those observed in DGBI in humans. These effects are mediated, in part, by alterations to glial prostaglandin and endocannabinoid signaling. Together, these data identify enteric glia as a cellular integration site through which DGBI risk factors produce changes in gut physiology and suggest that manipulating glial signaling may represent an attractive target for sex-specific therapeutic strategies in DGBIs.
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11
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Sheehan PW, Fass S, Sapkota D, Kang S, Hollis HC, Lawrence JH, Anafi RC, Dougherty JD, Fryer JD, Musiek ES. A glial circadian gene expression atlas reveals cell type and disease-specific reprogramming in response to amyloid pathology or aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596297. [PMID: 38853870 PMCID: PMC11160685 DOI: 10.1101/2024.05.28.596297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
While circadian rhythm disruption may promote neurodegenerative disease, how aging and neurodegenerative pathology impact circadian gene expression patterns in different brain cell types is unknown. Here, we used translating ribosome affinity purification methods to define the circadian translatomes of astrocytes, microglia, and bulk cerebral cortex, in healthy mouse brain and in the settings of amyloid-beta plaque pathology or aging. Our data reveal that glial circadian translatomes are highly cell type-specific and exhibit profound, context-dependent reprogramming of rhythmic transcripts in response to amyloid pathology or aging. Transcripts involved in glial activation, immunometabolism, and proteostasis, as well as nearly half of all Alzheimer Disease (AD)-associated risk genes, displayed circadian oscillations, many of which were altered by pathology. Amyloid-related differential gene expression was also dependent on time of day. Thus, circadian rhythms in gene expression are cell- and context dependent and provide important insights into glial gene regulation in health, AD, and aging.
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Affiliation(s)
- Patrick W. Sheehan
- Department of Neurology, Washington University School of Medicine, Saint Louis MO, USA
| | - Stuart Fass
- Department of Genetics, Washington University School of Medicine, Saint Louis MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis MO, USA
| | - Darshan Sapkota
- Department of Genetics, Washington University School of Medicine, Saint Louis MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis MO, USA
- Department of Biological Sciences and Department of Neuroscience, University of Texas at Dallas, Richardson, TX, USA
| | - Sylvia Kang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Henry C. Hollis
- School of Biomedical Engineering and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jennifer H. Lawrence
- Department of Neurology, Washington University School of Medicine, Saint Louis MO, USA
| | - Ron C. Anafi
- Department of Medicine, Chronobiology, and Sleep Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph D. Dougherty
- Department of Genetics, Washington University School of Medicine, Saint Louis MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis MO, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Jon D. Fryer
- Department of Neuroscience, Mayo Clinic, Scottsdale, AZ, USA
| | - Erik S. Musiek
- Department of Neurology, Washington University School of Medicine, Saint Louis MO, USA
- Center on Biological Rhythms and Sleep, Washington University School of Medicine, St. Louis, MO, USA
- Lead contact
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12
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Román ÁC, Benítez DA, Díaz-Pizarro A, Del Valle-Del Pino N, Olivera-Gómez M, Cumplido-Laso G, Carvajal-González JM, Mulero-Navarro S. Next generation sequencing technologies to address aberrant mRNA translation in cancer. NAR Cancer 2024; 6:zcae024. [PMID: 38751936 PMCID: PMC11094761 DOI: 10.1093/narcan/zcae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024] Open
Abstract
In this review, we explore the transformative impact of next generation sequencing technologies in the realm of translatomics (the study of how translational machinery acts on a genome-wide scale). Despite the expectation of a direct correlation between mRNA and protein content, the complex regulatory mechanisms that affect this relationship remark the limitations of standard RNA-seq approaches. Then, the review characterizes crucial techniques such as polysome profiling, ribo-seq, trap-seq, proximity-specific ribosome profiling, rnc-seq, tcp-seq, qti-seq and scRibo-seq. All these methods are summarized within the context of cancer research, shedding light on their applications in deciphering aberrant translation in cancer cells. In addition, we encompass databases and bioinformatic tools essential for researchers that want to address translatome analysis in the context of cancer biology.
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Affiliation(s)
- Ángel-Carlos Román
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Dixan A Benítez
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Alba Díaz-Pizarro
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Nuria Del Valle-Del Pino
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Marcos Olivera-Gómez
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Guadalupe Cumplido-Laso
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Jose M Carvajal-González
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
| | - Sonia Mulero-Navarro
- Departamento de Bioquímica y Biología Molecular y Genética, Universidad de Extremadura. Avda. de Elvas s/n, 06071 Badajoz, Spain
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13
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Bolívar S, Sanz E, Ovelleiro D, Zochodne DW, Udina E. Neuron-specific RNA-sequencing reveals different responses in peripheral neurons after nerve injury. eLife 2024; 12:RP91316. [PMID: 38742628 PMCID: PMC11093584 DOI: 10.7554/elife.91316] [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] [Indexed: 05/16/2024] Open
Abstract
Peripheral neurons are heterogeneous and functionally diverse, but all share the capability to switch to a pro-regenerative state after nerve injury. Despite the assumption that the injury response is similar among neuronal subtypes, functional recovery may differ. Understanding the distinct intrinsic regenerative properties between neurons may help to improve the quality of regeneration, prioritizing the growth of axon subpopulations to their targets. Here, we present a comparative analysis of regeneration across four key peripheral neuron populations: motoneurons, proprioceptors, cutaneous mechanoreceptors, and nociceptors. Using Cre/Ai9 mice that allow fluorescent labeling of neuronal subtypes, we found that nociceptors showed the greater regeneration after a sciatic crush, followed by motoneurons, mechanoreceptors, and, finally, proprioceptors. By breeding these Cre mice with Ribotag mice, we isolated specific translatomes and defined the regenerative response of these neuronal subtypes after axotomy. Only 20% of the regulated genes were common, revealing a diverse response to injury among neurons, which was also supported by the differential influence of neurotrophins among neuron subtypes. Among differentially regulated genes, we proposed MED12 as a specific regulator of the regeneration of proprioceptors. Altogether, we demonstrate that the intrinsic regenerative capacity differs between peripheral neuron subtypes, opening the door to selectively modulate these responses.
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Affiliation(s)
- Sara Bolívar
- Institute of Neurosciences, and Department Cell Biology, Physiology and Immunology, Universitat Autònoma de BarcelonaBellaterraSpain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Instituto de Salud Carlos IIIMadridSpain
| | - Elisenda Sanz
- Institute of Neurosciences, and Department Cell Biology, Physiology and Immunology, Universitat Autònoma de BarcelonaBellaterraSpain
| | - David Ovelleiro
- Peripheral Nervous System, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital CampusBarcelonaSpain
| | - Douglas W Zochodne
- Division of Neurology, Department of Medicine and the Neuroscience and Mental Health Institute, University of AlbertaEdmontonCanada
| | - Esther Udina
- Institute of Neurosciences, and Department Cell Biology, Physiology and Immunology, Universitat Autònoma de BarcelonaBellaterraSpain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Instituto de Salud Carlos IIIMadridSpain
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14
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Kapur M, Molumby MJ, Guzman C, Heinz S, Ackerman SL. Cell-type-specific expression of tRNAs in the brain regulates cellular homeostasis. Neuron 2024; 112:1397-1415.e6. [PMID: 38377989 PMCID: PMC11065635 DOI: 10.1016/j.neuron.2024.01.028] [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: 07/25/2023] [Revised: 12/23/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024]
Abstract
Defects in tRNA biogenesis are associated with multiple neurological disorders, yet our understanding of these diseases has been hampered by an inability to determine tRNA expression in individual cell types within a complex tissue. Here, we developed a mouse model in which RNA polymerase III is conditionally epitope tagged in a Cre-dependent manner, allowing us to accurately profile tRNA expression in any cell type in vivo. We investigated tRNA expression in diverse nervous system cell types, revealing dramatic heterogeneity in the expression of tRNA genes between populations. We found that while maintenance of levels of tRNA isoacceptor families is critical for cellular homeostasis, neurons are differentially vulnerable to insults to distinct tRNA isoacceptor families. Cell-type-specific translatome analysis suggests that the balance between tRNA availability and codon demand may underlie such differential resilience. Our work provides a platform for investigating the complexities of mRNA translation and tRNA biology in the brain.
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Affiliation(s)
- Mridu Kapur
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA; The Howard Hughes Medical Institute
| | - Michael J Molumby
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA; The Howard Hughes Medical Institute
| | - Carlos Guzman
- Department of Medicine, Division of Endocrinology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, Bioinformatics & Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sven Heinz
- Department of Medicine, Division of Endocrinology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, Bioinformatics & Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan L Ackerman
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA; The Howard Hughes Medical Institute; Department of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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15
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Martellucci S, Flütsch A, Carter M, Norimoto M, Pizzo D, Mantuano E, Sadri M, Wang Z, Chillin-Fuentes D, Rosenthal SB, Azmoon P, Gonias SL, Campana WM. Axon-derived PACSIN1 binds to the Schwann cell survival receptor, LRP1, and transactivates TrkC to promote gliatrophic activities. Glia 2024; 72:916-937. [PMID: 38372375 DOI: 10.1002/glia.24510] [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: 07/09/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 02/20/2024]
Abstract
Schwann cells (SCs) undergo phenotypic transformation and then orchestrate nerve repair following PNS injury. The ligands and receptors that activate and sustain SC transformation remain incompletely understood. Proteins released by injured axons represent important candidates for activating the SC Repair Program. The low-density lipoprotein receptor-related protein-1 (LRP1) is acutely up-regulated in SCs in response to injury, activating c-Jun, and promoting SC survival. To identify novel LRP1 ligands released in PNS injury, we applied a discovery-based approach in which extracellular proteins in the injured nerve were captured using Fc-fusion proteins containing the ligand-binding motifs of LRP1 (CCR2 and CCR4). An intracellular neuron-specific protein, Protein Kinase C and Casein Kinase Substrate in Neurons (PACSIN1) was identified and validated as an LRP1 ligand. Recombinant PACSIN1 activated c-Jun and ERK1/2 in cultured SCs. Silencing Lrp1 or inhibiting the LRP1 cell-signaling co-receptor, the NMDA-R, blocked the effects of PACSIN1 on c-Jun and ERK1/2 phosphorylation. Intraneural injection of PACSIN1 into crush-injured sciatic nerves activated c-Jun in wild-type mice, but not in mice in which Lrp1 is conditionally deleted in SCs. Transcriptome profiling of SCs revealed that PACSIN1 mediates gene expression events consistent with transformation to the repair phenotype. PACSIN1 promoted SC migration and viability following the TNFα challenge. When Src family kinases were pharmacologically inhibited or the receptor tyrosine kinase, TrkC, was genetically silenced or pharmacologically inhibited, PACSIN1 failed to induce cell signaling and prevent SC death. Collectively, these studies demonstrate that PACSIN1 is a novel axon-derived LRP1 ligand that activates SC repair signaling by transactivating TrkC.
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Affiliation(s)
- Stefano Martellucci
- Department of Anesthesiology, University of California San Diego, La Jolla, California, USA
| | - Andreas Flütsch
- Department of Anesthesiology, University of California San Diego, La Jolla, California, USA
| | - Mark Carter
- Department of Anesthesiology, University of California San Diego, La Jolla, California, USA
| | - Masaki Norimoto
- Department of Anesthesiology, University of California San Diego, La Jolla, California, USA
| | - Donald Pizzo
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Elisabetta Mantuano
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Mahrou Sadri
- Department of Anesthesiology, University of California San Diego, La Jolla, California, USA
| | - Zixuan Wang
- Department of Anesthesiology, University of California San Diego, La Jolla, California, USA
| | - Daisy Chillin-Fuentes
- Center for Computational Biology & Bioinformatics, Altman Clinical & Translational Research Institute, University of California San Diego, La Jolla, California, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, Altman Clinical & Translational Research Institute, University of California San Diego, La Jolla, California, USA
| | - Pardis Azmoon
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Steven L Gonias
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Wendy M Campana
- Department of Anesthesiology, University of California San Diego, La Jolla, California, USA
- Program in Neurosciences, University of California San Diego, La Jolla, California, USA
- Division of Research, San Diego VA Health Care System, San Diego, California, USA
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16
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Wu ST, Feng Y, Song R, Qi Y, Li L, Lu D, Wang Y, Wu W, Morgan A, Wang X, Xia Y, Liu R, Alexander SI, Wong J, Zhang Y, Zheng X. Foxp1 Is Required for Renal Intercalated Cell Differentiation and Acid-Base Regulation. J Am Soc Nephrol 2024; 35:533-548. [PMID: 38332484 PMCID: PMC11149051 DOI: 10.1681/asn.0000000000000319] [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: 08/02/2023] [Accepted: 02/05/2024] [Indexed: 02/10/2024] Open
Abstract
Key Points Foxp1 is a key transcriptional factor for the differentiation of intercalated cells in collecting ducts. Dmrt2 and Hmx2 act downstream of Foxp1 to control the differentiation of type A and type B intercalated cells, respectively. Foxp1 and Dmrt2 are essential for body acid–base balance regulation. Background Kidney collecting ducts comprise principal cells and intercalated cells, with intercalated cells playing a crucial role in kidney acid–base regulation through H+ and HCO3− secretion. Despite its significance, the molecular mechanisms controlling intercalated cell development remain incompletely understood. Methods To investigate the specific role of Foxp1 in kidney tubular system, we specifically deleted Foxp1 expression in kidney distal nephrons and collecting ducts. We examined the effects of Foxp1 on intercalated cell differentiation and urine acidification. RNA sequencing and Chip-seq were used to identify Foxp1 target genes. To dissect the genetic network that regulates intercalated cell differentiation, Dmrt2 -deficient mice were generated to determine the role of Dmrt2 in intercalated cell differentiation. Foxp1 -deficient mice were crossed with Notch2 -deficient mice to dissect the relation between Foxp1 and Notch signaling. Results Foxp1 was selectively expressed in intercalated cells in collecting ducts. The absence of Foxp1 in kidney tubules led to the abolishment of intercalated cell differentiation in the collecting ducts, resulting in distal renal tubular acidosis. Foxp1 regulates the expression of Dmrt2 and Hmx2 , two genes encoding transcription factors specifically expressed in type A and type B intercalated cell cells, respectively. Further genetic analysis revealed that Dmrt2 was essential for type A intercalated cell differentiation, and Foxp1 was necessary downstream of Notch for the regulation of intercalated cell differentiation. Conclusions Foxp1 is required for the renal intercalated cell differentiation and participated in acid–base regulation. Foxp1 regulated downstream transcriptional factors, Dmrt2 and Hmx2, which were involved in the specification of distinct subsets of intercalated cells.
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Affiliation(s)
- Shi-Ting Wu
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, and Center for Cardiovascular Diseases, Tianjin Medical University, Tianjin, China
| | - Yu Feng
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, and Center for Cardiovascular Diseases, Tianjin Medical University, Tianjin, China
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute and the Faulty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Yanmiao Qi
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, and Center for Cardiovascular Diseases, Tianjin Medical University, Tianjin, China
| | - Lin Li
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, and Center for Cardiovascular Diseases, Tianjin Medical University, Tianjin, China
| | - Dongbo Lu
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, and Center for Cardiovascular Diseases, Tianjin Medical University, Tianjin, China
| | - Yixuan Wang
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, and Center for Cardiovascular Diseases, Tianjin Medical University, Tianjin, China
| | - Wenrun Wu
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Angela Morgan
- Murdoch Children's Research Institute, The Royal Children's Hospital and Department of Audiology and Speech Pathology and Department of Pediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Xiaohong Wang
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, and Center for Cardiovascular Diseases, Tianjin Medical University, Tianjin, China
| | - Yin Xia
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Renjing Liu
- Vascular Epigenetics Laboratory, Victor Chang Cardiac Research Institute and School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Stephen I. Alexander
- Department of Pediatric Nephrology, The Children's Hospital at Westmead and Centre for Kidney Research, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Justin Wong
- Epigenetics and RNA Biology Program Centenary Institute and the Faulty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Yuzhen Zhang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiangjian Zheng
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, and Center for Cardiovascular Diseases, Tianjin Medical University, Tianjin, China
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17
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Aranda ML, Bhoi JD, Parra OAP, Lee SK, Yamada T, Yang Y, Schmidt TM. Genetic tuning of intrinsically photosensitive retinal ganglion cell subtype identity to drive visual behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.590656. [PMID: 38712084 PMCID: PMC11071530 DOI: 10.1101/2024.04.25.590656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The melanopsin-expressing, intrinsically photosensitive retinal ganglion cells (ipRGCs) comprise a subset of the ∼40 retinal ganglion cell types in the mouse retina and drive a diverse array of light-evoked behaviors from circadian photoentrainment to pupil constriction to contrast sensitivity for visual perception. Central to the ability of ipRGCs to control this diverse array of behaviors is the distinct complement of morphophysiological features and gene expression patterns found in the M1-M6 ipRGC subtypes. However, the genetic regulatory programs that give rise to subtypes of ipRGCs are unknown. Here, we identify the transcription factor Brn3b (Pou4f2) as a key genetic regulator that shapes the unique functions of ipRGC subtypes and their diverse downstream visual behaviors.
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18
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Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev 2024; 124:4734-4777. [PMID: 38579177 PMCID: PMC11046439 DOI: 10.1021/acs.chemrev.3c00575] [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: 08/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 04/07/2024]
Abstract
This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNA-mediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.
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Affiliation(s)
- Elsa Zacco
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Laura Broglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Misuzu Kurihara
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Michele Monti
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Stefano Gustincich
- Central
RNA Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Annalisa Pastore
- UK
Dementia Research Institute at the Maurice Wohl Institute of King’s
College London, London SE5 9RT, U.K.
| | - Kathrin Plath
- Department
of Biological Chemistry, David Geffen School
of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shinichi Nagakawa
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Andrea Cerase
- Blizard
Institute,
Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, U.K.
- Unit
of Cell and developmental Biology, Department of Biology, Università di Pisa, 56123 Pisa, Italy
| | - Natalia Sanchez de Groot
- Unitat
de Bioquímica, Departament de Bioquímica i Biologia
Molecular, Universitat Autònoma de
Barcelona, 08193 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
- Catalan
Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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19
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Kim HD, Wei J, Call T, Ma X, Quintus NT, Summers AJ, Carotenuto S, Johnson R, Nguyen A, Cui Y, Park JG, Qiu S, Ferguson D. SIRT1 Coordinates Transcriptional Regulation of Neural Activity and Modulates Depression-Like Behaviors in the Nucleus Accumbens. Biol Psychiatry 2024:S0006-3223(24)01176-4. [PMID: 38575105 DOI: 10.1016/j.biopsych.2024.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Major depression and anxiety disorders are significant causes of disability and socioeconomic burden. Despite the prevalence and considerable impact of these affective disorders, their pathophysiology remains elusive. Thus, there is an urgent need to develop novel therapeutics for these conditions. We evaluated the role of SIRT1 in regulating dysfunctional processes of reward by using chronic social defeat stress to induce depression- and anxiety-like behaviors. Chronic social defeat stress induces physiological and behavioral changes that recapitulate depression-like symptomatology and alters gene expression programs in the nucleus accumbens, but cell type-specific changes in this critical structure remain largely unknown. METHODS We examined transcriptional profiles of D1-expressing medium spiny neurons (MSNs) lacking deacetylase activity of SIRT1 by RNA sequencing in a cell type-specific manner using the RiboTag line of mice. We analyzed differentially expressed genes using gene ontology tools including SynGO and EnrichR and further demonstrated functional changes in D1-MSN-specific SIRT1 knockout (KO) mice using electrophysiological and behavioral measurements. RESULTS RNA sequencing revealed altered transcriptional profiles of D1-MSNs lacking functional SIRT1 and showed specific changes in synaptic genes including glutamatergic and GABAergic (gamma-aminobutyric acidergic) receptors in D1-MSNs. These molecular changes may be associated with decreased excitatory and increased inhibitory neural activity in Sirt1 KO D1-MSNs, accompanied by morphological changes. Moreover, the D1-MSN-specific Sirt1 KO mice exhibited proresilient changes in anxiety- and depression-like behaviors. CONCLUSIONS SIRT1 coordinates excitatory and inhibitory synaptic genes to regulate the GABAergic output tone of D1-MSNs. These findings reveal a novel signaling pathway that has potential for the development of innovative treatments for affective disorders.
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Affiliation(s)
- Hee-Dae Kim
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona
| | - Jing Wei
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona
| | - Tanessa Call
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona
| | - Xiaokuang Ma
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona
| | - Nicole Teru Quintus
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona
| | - Alexander J Summers
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona
| | - Samantha Carotenuto
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona
| | - Ross Johnson
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona
| | - Angel Nguyen
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona
| | - Yuehua Cui
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona
| | - Jin G Park
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Shenfeng Qiu
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona
| | - Deveroux Ferguson
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona.
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20
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Hose L, Langenhagen AK, Kefalakes E, Schweitzer T, Kubinski S, Barak S, Pich A, Grothe C. A dual-omics approach on the effects of fibroblast growth factor-2 (FGF-2) on ventral tegmental area dopaminergic neurons in response to alcohol consumption in mice. Eur J Neurosci 2024; 59:1519-1535. [PMID: 38185886 DOI: 10.1111/ejn.16234] [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: 07/31/2023] [Revised: 11/25/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024]
Abstract
Harmful alcohol consumption is a major socioeconomic burden to the health system, as it can be the cause of mortality of heavy alcohol drinkers. The dopaminergic (DAergic) system is thought to play an important role in the pathogenesis of alcohol drinking behaviour; however, its exact role remains elusive. Fibroblast growth factor 2 (FGF-2), a neurotrophic factor, associated with both the DAergic system and alcohol consumption, may play an important role in DAergic neuroadaptations during alcohol abuse. Within this study, we aimed to clarify the role of endogenous FGF-2 on the DAergic system and whether there is a possible link to alcohol consumption. We found that lack of FGF-2 reduces the alcohol intake of mice. Transcriptome analysis of DAergic neurons revealed that FGF-2 knockout (FGF-2 KO) shifts the molecular fingerprint of midbrain dopaminergic (mDA) neurons to DA subtypes of the ventral tegmental area (VTA). In line with this, proteomic changes predominantly appear also in the VTA. Interestingly, these changes led to an altered regulation of the FGF-2 signalling cascades and DAergic pathways in a region-specific manner, which was only marginally affected by voluntary alcohol consumption. Thus, lack of FGF-2 not only affects the gene expression but also the proteome of specific brain regions of mDA neurons. Our study provides new insights into the neuroadaptations of the DAergic system during alcohol abuse and, therefore, comprises novel targets for future pharmacological interventions.
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Affiliation(s)
- Leonie Hose
- Hannover Medical School, Institute of Neuroanatomy and Cell Biology, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Alina Katharina Langenhagen
- Hannover Medical School, Institute of Neuroanatomy and Cell Biology, Hannover, Germany
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Ekaterini Kefalakes
- Hannover Medical School, Institute of Neuroanatomy and Cell Biology, Hannover, Germany
| | - Theresa Schweitzer
- Institute of Toxicology, Hannover, Germany
- Core Facility Proteomics, Institute of Toxicology, Hannover, Germany
| | - Sabrina Kubinski
- Hannover Medical School, Institute of Neuroanatomy and Cell Biology, Hannover, Germany
| | - Segev Barak
- School of Psychological Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Andreas Pich
- Institute of Toxicology, Hannover, Germany
- Core Facility Proteomics, Institute of Toxicology, Hannover, Germany
| | - Claudia Grothe
- Hannover Medical School, Institute of Neuroanatomy and Cell Biology, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
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21
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McCallum S, Suresh KB, Islam T, Saustad AW, Shelest O, Patil A, Lee D, Kwon B, Yenokian I, Kawaguchi R, Beveridge CH, Manchandra P, Randolph CE, Meares GP, Dutta R, Plummer J, Knott SRV, Chopra G, Burda JE. Lesion-remote astrocytes govern microglia-mediated white matter repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585251. [PMID: 38558977 PMCID: PMC10979953 DOI: 10.1101/2024.03.15.585251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Spared regions of the damaged central nervous system undergo dynamic remodeling and exhibit a remarkable potential for therapeutic exploitation. Here, lesion-remote astrocytes (LRAs), which interact with viable neurons, glia and neural circuitry, undergo reactive transformations whose molecular and functional properties are poorly understood. Using multiple transcriptional profiling methods, we interrogated LRAs from spared regions of mouse spinal cord following traumatic spinal cord injury (SCI). We show that LRAs acquire a spectrum of molecularly distinct, neuroanatomically restricted reactivity states that evolve after SCI. We identify transcriptionally unique reactive LRAs in degenerating white matter that direct the specification and function of local microglia that clear lipid-rich myelin debris to promote tissue repair. Fueling this LRA functional adaptation is Ccn1 , which encodes for a secreted matricellular protein. Loss of astrocyte CCN1 leads to excessive, aberrant activation of local microglia with (i) abnormal molecular specification, (ii) dysfunctional myelin debris processing, and (iii) impaired lipid metabolism, culminating in blunted debris clearance and attenuated neurological recovery from SCI. Ccn1 -expressing white matter astrocytes are specifically induced by local myelin damage and generated in diverse demyelinating disorders in mouse and human, pointing to their fundamental, evolutionarily conserved role in white matter repair. Our findings show that LRAs assume regionally divergent reactivity states with functional adaptations that are induced by local context-specific triggers and influence disorder outcome. Astrocytes tile the central nervous system (CNS) where they serve vital roles that uphold healthy nervous system function, including regulation of synapse development, buffering of neurotransmitters and ions, and provision of metabolic substrates 1 . In response to diverse CNS insults, astrocytes exhibit disorder-context specific transformations that are collectively referred to as reactivity 2-5 . The characteristics of regionally and molecularly distinct reactivity states are incompletely understood. The mechanisms through which distinct reactivity states arise, how they evolve or resolve over time, and their consequences for local cell function and CNS disorder progression remain enigmatic. Immediately adjacent to CNS lesions, border-forming astrocytes (BFAs) undergo transcriptional reprogramming and proliferation to form a neuroprotective barrier that restricts inflammation and supports axon regeneration 6-9 . Beyond the lesion, spared but dynamic regions of the injured CNS exhibit varying degrees of synaptic circuit remodeling and progressive cellular responses to secondary damage that have profound consequences for neural repair and recovery 10,11 . Throughout these cytoarchitecturally intact, but injury-reactive regions, lesion-remote astrocytes (LRAs) intermingle with neurons and glia, undergo little to no proliferation, and exhibit varying degrees of cellular hypertrophy 7,12,13 . The molecular and functional properties of LRAs remain grossly undefined. Therapeutically harnessing spared regions of the injured CNS will require a clearer understanding of the accompanying cellular and molecular landscape. Here, we leveraged integrative transcriptional profiling methodologies to identify multiple spatiotemporally resolved, molecularly distinct states of LRA reactivity within the injured spinal cord. Computational modeling of LRA-mediated heterotypic cell interactions, astrocyte-specific conditional gene deletion, and multiple mouse models of acute and chronic CNS white matter degeneration were used to interrogate a newly identified white matter degeneration-reactive astrocyte subtype. We define how this reactivity state is induced and its role in governing the molecular and functional specification of local microglia that clear myelin debris from the degenerating white matter to promote repair.
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22
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Sancho L, Boisvert MM, Dawoodtabar T, Burgado J, Wang E, Allen NJ. Astrocyte CCN1 stabilizes neural circuits in the adult brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.585077. [PMID: 38559139 PMCID: PMC10979986 DOI: 10.1101/2024.03.14.585077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Neural circuits in many brain regions are refined by experience. Sensory circuits support higher plasticity at younger ages during critical periods - times of circuit refinement and maturation - and limit plasticity in adulthood for circuit stability. The mechanisms underlying these differing plasticity levels and how they serve to maintain and stabilize the properties of sensory circuits remain largely unclear. By combining a transcriptomic approach with ex vivo electrophysiology and in vivo imaging techniques, we identify that astrocytes release cellular communication network factor 1 (CCN1) to maintain synapse and circuit stability in the visual cortex. By overexpressing CCN1 in critical period astrocytes, we find that it promotes the maturation of inhibitory circuits and limits ocular dominance plasticity. Conversely, by knocking out astrocyte CCN1 in adults, binocular circuits are destabilized. These studies establish CCN1 as a novel astrocyte-secreted factor that stabilizes neuronal circuits. Moreover, they demonstrate that the composition and properties of sensory circuits require ongoing maintenance in adulthood, and that these maintenance cues are provided by astrocytes.
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23
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Price NL, Fernández-Tussy P, Varela L, Cardelo MP, Shanabrough M, Aryal B, de Cabo R, Suárez Y, Horvath TL, Fernández-Hernando C. microRNA-33 controls hunger signaling in hypothalamic AgRP neurons. Nat Commun 2024; 15:2131. [PMID: 38459068 PMCID: PMC10923783 DOI: 10.1038/s41467-024-46427-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 02/21/2024] [Indexed: 03/10/2024] Open
Abstract
AgRP neurons drive hunger, and excessive nutrient intake is the primary driver of obesity and associated metabolic disorders. While many factors impacting central regulation of feeding behavior have been established, the role of microRNAs in this process is poorly understood. Utilizing unique mouse models, we demonstrate that miR-33 plays a critical role in the regulation of AgRP neurons, and that loss of miR-33 leads to increased feeding, obesity, and metabolic dysfunction in mice. These effects include the regulation of multiple miR-33 target genes involved in mitochondrial biogenesis and fatty acid metabolism. Our findings elucidate a key regulatory pathway regulated by a non-coding RNA that impacts hunger by controlling multiple bioenergetic processes associated with the activation of AgRP neurons, providing alternative therapeutic approaches to modulate feeding behavior and associated metabolic diseases.
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Affiliation(s)
- Nathan L Price
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and System Metabolism. Yale University School of Medicine, New Haven, CT, USA
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Pablo Fernández-Tussy
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and System Metabolism. Yale University School of Medicine, New Haven, CT, USA
| | - Luis Varela
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and System Metabolism. Yale University School of Medicine, New Haven, CT, USA
- Laboratory of Glia -Neuron Interactions in the control of Hunger. Achucarro Basque Center for Neuroscience, 48940, Leioa, Vizcaya, Spain
- IKERBASQUE, Basque Foundation for Science, 48009, Bilbao, Vizcaya, Spain
| | - Magdalena P Cardelo
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and System Metabolism. Yale University School of Medicine, New Haven, CT, USA
| | - Marya Shanabrough
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Binod Aryal
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and System Metabolism. Yale University School of Medicine, New Haven, CT, USA
| | - Rafael de Cabo
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Yajaira Suárez
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and System Metabolism. Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology. Yale University School of Medicine, New Haven, CT, USA
| | - Tamas L Horvath
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA.
- Yale Center for Molecular and System Metabolism. Yale University School of Medicine, New Haven, CT, USA.
- Laboratory of Glia -Neuron Interactions in the control of Hunger. Achucarro Basque Center for Neuroscience, 48940, Leioa, Vizcaya, Spain.
- IKERBASQUE, Basque Foundation for Science, 48009, Bilbao, Vizcaya, Spain.
- Department of Neuroscience. Yale University School of Medicine, New Haven, CT, USA.
| | - Carlos Fernández-Hernando
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA.
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA.
- Yale Center for Molecular and System Metabolism. Yale University School of Medicine, New Haven, CT, USA.
- Department of Pathology. Yale University School of Medicine, New Haven, CT, USA.
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24
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Asghari Adib E, Shadrach JL, Reilly-Jankowiak L, Dwivedi MK, Rogers AE, Shahzad S, Passino R, Giger RJ, Pierchala BA, Collins CA. DLK signaling in axotomized neurons triggers complement activation and loss of upstream synapses. Cell Rep 2024; 43:113801. [PMID: 38363678 PMCID: PMC11088462 DOI: 10.1016/j.celrep.2024.113801] [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: 09/26/2022] [Revised: 12/27/2023] [Accepted: 01/31/2024] [Indexed: 02/18/2024] Open
Abstract
Axotomized spinal motoneurons (MNs) lose presynaptic inputs following peripheral nerve injury; however, the cellular mechanisms that lead to this form of synapse loss are currently unknown. Here, we delineate a critical role for neuronal kinase dual leucine zipper kinase (DLK)/MAP3K12, which becomes activated in axotomized neurons. Studies with conditional knockout mice indicate that DLK signaling activation in injured MNs triggers the induction of phagocytic microglia and synapse loss. Aspects of the DLK-regulated response include expression of C1q first from the axotomized MN and then later in surrounding microglia, which subsequently phagocytose presynaptic components of upstream synapses. Pharmacological ablation of microglia inhibits the loss of cholinergic C boutons from axotomized MNs. Together, the observations implicate a neuronal mechanism, governed by the DLK, in the induction of inflammation and the removal of synapses.
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Affiliation(s)
- Elham Asghari Adib
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA; Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Jennifer L Shadrach
- Department of Biologic and Materials Sciences, University of Michigan, Ann Arbor, MI, USA
| | | | - Manish K Dwivedi
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Abigail E Rogers
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Shameena Shahzad
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ryan Passino
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Roman J Giger
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Brian A Pierchala
- Department of Biologic and Materials Sciences, University of Michigan, Ann Arbor, MI, USA; Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Catherine A Collins
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA; Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA.
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25
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Sugimoto C, Perna MK, Regan SL, Tepe EA, Liou R, Fritz AL, Williams MT, Vorhees CV, Skelton MR. A Gad2 specific Slc6a8 deletion recapitulates the contextual and cued freezing deficits seen in Slc6a8 -/y mice. Brain Res 2024; 1825:148690. [PMID: 38030104 PMCID: PMC10875619 DOI: 10.1016/j.brainres.2023.148690] [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: 08/21/2023] [Revised: 11/14/2023] [Accepted: 11/25/2023] [Indexed: 12/01/2023]
Abstract
The creatine (Cr)-phosphocreatine shuttle is essential for ATP homeostasis. In humans, the absence of brain Cr causes significant intellectual disability, epilepsy, and language delay. Mutations of the creatine transporter (SLC6A8) are the most common cause of Cr deficiency. In rodents, Slc6a8 deletion causes deficits in spatial learning, novel object recognition (NOR), as well as in contextual and cued freezing. The mechanisms that underlie these cognitive deficits are not known. Due to the heterogeneous nature of the brain, it is important to determine which systems are affected by a loss of Cr. In this study, we generated mice lacking Slc6a8 in GABAergic neurons by crossing Slc6a8FL mice with Gad2-Cre mice. These Gad2-specific Slc6a8 knockout (cKO) mice, along with the ubiquitous Slc6a8 KO (Slc6a8-/y), Gad2-Cre+, and wild-type (WT) mice were tested in the Morris water maze, NOR, conditioned freezing, and the radial water maze. Similar to the Slc6a8-/y mice, cKO mice had reduced contextual and cued freezing compared with WT mice. The cKO mice had a mild spatial learning deficit during the reversal phase of the MWM, however they were not as pronounced as in Slc6a8-/y mice. In NOR, the Gad2-Cre mice spent less time with the novel object, similar to the reduced novel time in the cKO mice. There were no changes in radial water maze performance. Slc6a8 deletion in GABAergic neurons is sufficient to recapitulate the conditioned freezing deficits seen in Slc6a8-/y mice.
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Affiliation(s)
- Chiho Sugimoto
- Department of Pediatrics, University of Cincinnati College of Medicine and Division of Neurology, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, United States
| | - Marla K Perna
- Department of Pediatrics, University of Cincinnati College of Medicine and Division of Neurology, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, United States.
| | - Samantha L Regan
- Department of Pediatrics, University of Cincinnati College of Medicine and Division of Neurology, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, United States.
| | - Erin A Tepe
- Department of Pediatrics, University of Cincinnati College of Medicine and Division of Neurology, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, United States
| | - Rosalyn Liou
- Department of Pediatrics, University of Cincinnati College of Medicine and Division of Neurology, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, United States.
| | - Adam L Fritz
- Department of Pediatrics, University of Cincinnati College of Medicine and Division of Neurology, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, United States
| | - Michael T Williams
- Department of Pediatrics, University of Cincinnati College of Medicine and Division of Neurology, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, United States.
| | - Charles V Vorhees
- Department of Pediatrics, University of Cincinnati College of Medicine and Division of Neurology, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, United States.
| | - Matthew R Skelton
- Department of Pediatrics, University of Cincinnati College of Medicine and Division of Neurology, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, United States.
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26
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Cissé YM, Montgomery KR, Zierden HC, Hill EM, Kane PJ, Huang W, Kane MA, Bale TL. Maternal preconception stress produces sex-specific effects at the maternal:fetal interface to impact offspring development and phenotypic outcomes†. Biol Reprod 2024; 110:339-354. [PMID: 37971364 PMCID: PMC10873277 DOI: 10.1093/biolre/ioad156] [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] [Indexed: 11/19/2023] Open
Abstract
Entering pregnancy with a history of adversity, including adverse childhood experiences and racial discrimination stress, is a predictor of negative maternal and fetal health outcomes. Little is known about the biological mechanisms by which preconception adverse experiences are stored and impact future offspring health outcomes. In our maternal preconception stress (MPS) model, female mice underwent chronic stress from postnatal days 28-70 and were mated 2 weeks post-stress. Maternal preconception stress dams blunted the pregnancy-induced shift in the circulating extracellular vesicle proteome and reduced glucose tolerance at mid-gestation, suggesting a shift in pregnancy adaptation. To investigate MPS effects at the maternal:fetal interface, we probed the mid-gestation placental, uterine, and fetal brain tissue transcriptome. Male and female placentas differentially regulated expression of genes involved in growth and metabolic signaling in response to gestation in an MPS dam. We also report novel offspring sex- and MPS-specific responses in the uterine tissue apposing these placentas. In the fetal compartment, MPS female offspring reduced expression of neurodevelopmental genes. Using a ribosome-tagging transgenic approach we detected a dramatic increase in genes involved in chromatin regulation in a PVN-enriched neuronal population in females at PN21. While MPS had an additive effect on high-fat-diet (HFD)-induced weight gain in male offspring, both MPS and HFD were necessary to induce significant weight gain in female offspring. These data highlight the preconception period as a determinant of maternal health in pregnancy and provides novel insights into mechanisms by which maternal stress history impacts offspring developmental programming.
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Affiliation(s)
- Yasmine M Cissé
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kristen R Montgomery
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Hannah C Zierden
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Elizabeth M Hill
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Patrick J Kane
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - Tracy L Bale
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
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27
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Jackson WS, Bauer S, Kaczmarczyk L, Magadi SS. Selective Vulnerability to Neurodegenerative Disease: Insights from Cell Type-Specific Translatome Studies. BIOLOGY 2024; 13:67. [PMID: 38392286 PMCID: PMC10886597 DOI: 10.3390/biology13020067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/24/2024]
Abstract
Neurodegenerative diseases (NDs) manifest a wide variety of clinical symptoms depending on the affected brain regions. Gaining insights into why certain regions are resistant while others are susceptible is vital for advancing therapeutic strategies. While gene expression changes offer clues about disease responses across brain regions, the mixture of cell types therein obscures experimental results. In recent years, methods that analyze the transcriptomes of individual cells (e.g., single-cell RNA sequencing or scRNAseq) have been widely used and have provided invaluable insights into specific cell types. Concurrently, transgene-based techniques that dissect cell type-specific translatomes (CSTs) in model systems, like RiboTag and bacTRAP, offer unique advantages but have received less attention. This review juxtaposes the merits and drawbacks of both methodologies, focusing on the use of CSTs in understanding conditions like amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), Alzheimer's disease (AD), and specific prion diseases like fatal familial insomnia (FFI), genetic Creutzfeldt-Jakob disease (gCJD), and acquired prion disease. We conclude by discussing the emerging trends observed across multiple diseases and emerging methods.
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Affiliation(s)
- Walker S Jackson
- Wallenberg Center for Molecular Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Susanne Bauer
- Wallenberg Center for Molecular Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Lech Kaczmarczyk
- Wallenberg Center for Molecular Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Srivathsa S Magadi
- Wallenberg Center for Molecular Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
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28
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Caccavano AP, Kimmel S, Vlachos A, Mahadevan V, Kim JH, Vargish G, Chittajallu R, London E, Yuan X, Hunt S, Eldridge MAG, Cummins AC, Hines BE, Plotnikova A, Mohanty A, Averbeck BB, Zaghloul K, Dimidschstein J, Fishell G, Pelkey KA, McBain CJ. Divergent opioid-mediated suppression of inhibition between hippocampus and neocortex across species and development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576455. [PMID: 38313283 PMCID: PMC10836073 DOI: 10.1101/2024.01.20.576455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Opioid receptors within the CNS regulate pain sensation and mood and are key targets for drugs of abuse. Within the adult rodent hippocampus (HPC), μ-opioid receptor agonists suppress inhibitory parvalbumin-expressing interneurons (PV-INs), thus disinhibiting the circuit. However, it is uncertain if this disinhibitory motif is conserved in other cortical regions, species, or across development. We observed that PV-IN mediated inhibition is robustly suppressed by opioids in HPC but not neocortex in mice and nonhuman primates, with spontaneous inhibitory tone in resected human tissue also following a consistent dichotomy. This hippocampal disinhibitory motif was established in early development when immature PV-INs and opioids already influence primordial network rhythmogenesis. Acute opioid-mediated modulation was partially occluded with morphine pretreatment, with implications for the effects of opioids on hippocampal network activity during circuit maturation as well as learning and memory. Together, these findings demonstrate that PV-INs exhibit a divergence in opioid sensitivity across brain regions that is remarkably conserved across evolution and highlights the underappreciated role of opioids acting through immature PV-INs in shaping hippocampal development.
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Affiliation(s)
- Adam P Caccavano
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sarah Kimmel
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Anna Vlachos
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Vivek Mahadevan
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - June Hoan Kim
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Geoffrey Vargish
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Ramesh Chittajallu
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Edra London
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Xiaoqing Yuan
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Steven Hunt
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Alex C Cummins
- National Institute of Mental Health (NIMH), NIH, Bethesda, MD, USA
| | - Brendan E Hines
- National Institute of Mental Health (NIMH), NIH, Bethesda, MD, USA
| | - Anya Plotnikova
- National Institute of Mental Health (NIMH), NIH, Bethesda, MD, USA
| | - Arya Mohanty
- National Institute of Mental Health (NIMH), NIH, Bethesda, MD, USA
| | - Bruno B Averbeck
- National Institute of Mental Health (NIMH), NIH, Bethesda, MD, USA
| | - Kareem Zaghloul
- National Institute of Neurological Disorders and Stroke (NINDS) Intramural Research Program, NIH Bethesda, MD, USA
| | - Jordane Dimidschstein
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gord Fishell
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Kenneth A Pelkey
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Chris J McBain
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
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Cochran JD, Leathers TA, Maldosevic E, Siejda KW, Vitello J, Lee H, Bradley LA, Young A, Jomaa A, Wolf MJ. Cell cycle specific, differentially tagged ribosomal proteins to measure phase specific transcriptomes from asynchronously cycling cells. Sci Rep 2024; 14:1623. [PMID: 38238470 PMCID: PMC10796924 DOI: 10.1038/s41598-024-52085-5] [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: 02/02/2023] [Accepted: 01/13/2024] [Indexed: 01/22/2024] Open
Abstract
Asynchronously cycling cells pose a challenge to the accurate characterization of phase-specific gene expression. Current strategies, including RNAseq, survey the steady state gene expression across the cell cycle and are inherently limited by their inability to resolve dynamic gene regulatory networks. Single cell RNAseq (scRNAseq) can identify different cell cycle transcriptomes if enough cycling cells are present, however some cells are not amenable to scRNAseq. Therefore, we merged two powerful strategies, the CDT1 and GMNN degrons used in Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) cell cycle sensors and the ribosomal protein epitope tagging used in RiboTrap/Tag technologies to isolate cell cycle phase-specific mRNA for sequencing. The resulting cell cycle dependent, tagged ribosomal proteins (ccTaggedRP) were differentially expressed during the cell cycle, had similar subcellular locations as endogenous ribosomal proteins, incorporated into ribosomes and polysomes, and facilitated the recovery of cell cycle phase-specific RNA for sequencing. ccTaggedRP has broad applications to investigate phase-specific gene expression in complex cell populations.
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Affiliation(s)
- Jesse D Cochran
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, USA
| | - Tess A Leathers
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, USA
| | - Emir Maldosevic
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Klara W Siejda
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Julian Vitello
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Haesol Lee
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Leigh A Bradley
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Alex Young
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Ahmad Jomaa
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Matthew J Wolf
- Department of Medicine, University of Virginia, Charlottesville, VA, USA.
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA.
- Division of Cardiology, University of Virginia, Medical Research Building 5 (MR5), Room G213, 415 Lane Road, Charlottesville, VA, 22908, USA.
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Griffin EN, Jucius T, Sim SE, Harris BS, Heinz S, Ackerman SL. RREB1 regulates neuronal proteostasis and the microtubule network. SCIENCE ADVANCES 2024; 10:eadh3929. [PMID: 38198538 PMCID: PMC10780896 DOI: 10.1126/sciadv.adh3929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
Transcription factors play vital roles in neuron development; however, little is known about the role of these proteins in maintaining neuronal homeostasis. Here, we show that the transcription factor RREB1 (Ras-responsive element-binding protein 1) is essential for neuron survival in the mammalian brain. A spontaneous mouse mutation causing loss of a nervous system-enriched Rreb1 transcript is associated with progressive loss of cerebellar Purkinje cells and ataxia. Analysis of chromatin immunoprecipitation and sequencing, along with RNA sequencing data revealed dysregulation of RREB1 targets associated with the microtubule cytoskeleton. In agreement with the known role of microtubules in dendritic development, dendritic complexity was disrupted in Rreb1-deficient neurons. Analysis of sequencing data also suggested that RREB1 plays a role in the endomembrane system. Mutant Purkinje cells had fewer numbers of autophagosomes and lysosomes and contained P62- and ubiquitin-positive inclusions. Together, these studies demonstrate that RREB1 functions to maintain the microtubule network and proteostasis in mammalian neurons.
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Affiliation(s)
- Emily N. Griffin
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thomas Jucius
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Su-Eon Sim
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Sven Heinz
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan L. Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
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31
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Song Y, Seward CH, Chen CY, LeBlanc A, Leddy AM, Stubbs L. Isolated loss of the AUTS2 long isoform, brain-wide or targeted to Calbindin-lineage cells, generates a specific suite of brain, behavioral, and molecular pathologies. Genetics 2024; 226:iyad182. [PMID: 37816306 PMCID: PMC10763537 DOI: 10.1093/genetics/iyad182] [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: 05/04/2023] [Revised: 09/25/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Rearrangements within the AUTS2 region are associated with a rare syndromic disorder with intellectual disability, developmental delay, and behavioral abnormalities as core features. In addition, smaller regional variants are linked to wide range of neuropsychiatric disorders, underscoring the gene's essential role in brain development. Like many essential neurodevelopmental genes, AUTS2 is large and complex, generating distinct long (AUTS2-l) and short (AUTS2-s) protein isoforms from alternative promoters. Although evidence suggests unique isoform functions, the contributions of each isoform to specific AUTS2-linked phenotypes have not been clearly resolved. Furthermore, Auts2 is widely expressed across the developing brain, but cell populations most central to disease presentation have not been determined. In this study, we focused on the specific roles of AUTS2-l in brain development, behavior, and postnatal brain gene expression, showing that brain-wide AUTS2-l ablation leads to specific subsets of the recessive pathologies associated with mutations in 3' exons (exons 8-19) that disrupt both major isoforms. We identify downstream genes that could explain expressed phenotypes including hundreds of putative direct AUTS2-l target genes. Furthermore, in contrast to 3' Auts2 mutations which lead to dominant hypoactivity, AUTS2-l loss-of-function is associated with dominant hyperactivity and repetitive behaviors, phenotypes exhibited by many human patients. Finally, we show that AUTS2-l ablation in Calbindin 1-expressing cell lineages is sufficient to yield learning/memory deficits and hyperactivity with abnormal dentate gyrus granule cell maturation, but not other phenotypic effects. These data provide new clues to in vivo AUTS2-l functions and novel information relevant to genotype-phenotype correlations in the human AUTS2 region.
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Affiliation(s)
- Yunshu Song
- Pacific Northwest Research Institute, Seattle WA 98122, USA
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Chih-Ying Chen
- Pacific Northwest Research Institute, Seattle WA 98122, USA
| | - Amber LeBlanc
- Pacific Northwest Research Institute, Seattle WA 98122, USA
| | | | - Lisa Stubbs
- Pacific Northwest Research Institute, Seattle WA 98122, USA
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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32
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Frumer GR, Shin SH, Jung S, Kim JS. Not just Glia-Dissecting brain macrophages in the mouse. Glia 2024; 72:5-18. [PMID: 37501579 DOI: 10.1002/glia.24445] [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: 04/06/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Macrophages have emerged as critical cellular components of the central nervous system (CNS), promoting development, maintenance, and immune defense of the CNS. Here we will review recent advances in our understanding of brain macrophage heterogeneity, including microglia and border-associated macrophages, focusing on the mouse. Emphasis will be given to the discussion of strengths and limitations of the experimental approaches that have led to the recent insights and hold promise to further deepen our mechanistic understanding of brain macrophages that might eventually allow to harness their activities for the management of CNS pathologies.
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Affiliation(s)
- Gal Ronit Frumer
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sun-Hye Shin
- 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
| | - Jung-Seok Kim
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
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33
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Day M, Belal M, Surmeier WC, Melendez A, Wokosin D, Tkatch T, Clarke VRJ, Surmeier DJ. GABAergic regulation of striatal spiny projection neurons depends upon their activity state. PLoS Biol 2024; 22:e3002483. [PMID: 38295323 PMCID: PMC10830145 DOI: 10.1371/journal.pbio.3002483] [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: 03/17/2023] [Accepted: 12/26/2023] [Indexed: 02/02/2024] Open
Abstract
Synaptic transmission mediated by GABAA receptors (GABAARs) in adult, principal striatal spiny projection neurons (SPNs) can suppress ongoing spiking, but its effect on synaptic integration at subthreshold membrane potentials is less well characterized, particularly those near the resting down-state. To fill this gap, a combination of molecular, optogenetic, optical, and electrophysiological approaches were used to study SPNs in mouse ex vivo brain slices, and computational tools were used to model somatodendritic synaptic integration. In perforated patch recordings, activation of GABAARs, either by uncaging of GABA or by optogenetic stimulation of GABAergic synapses, evoked currents with a reversal potential near -60 mV in both juvenile and adult SPNs. Transcriptomic analysis and pharmacological work suggested that this relatively positive GABAAR reversal potential was not attributable to NKCC1 expression, but rather to HCO3- permeability. Regardless, from down-state potentials, optogenetic activation of dendritic GABAergic synapses depolarized SPNs. This GABAAR-mediated depolarization summed with trailing ionotropic glutamate receptor (iGluR) stimulation, promoting dendritic spikes and increasing somatic depolarization. Simulations revealed that a diffuse dendritic GABAergic input to SPNs effectively enhanced the response to dendritic iGluR signaling and promoted dendritic spikes. Taken together, our results demonstrate that GABAARs can work in concert with iGluRs to excite adult SPNs when they are in the resting down-state, suggesting that their inhibitory role is limited to brief periods near spike threshold. This state-dependence calls for a reformulation for the role of intrastriatal GABAergic circuits.
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Affiliation(s)
- Michelle Day
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Marziyeh Belal
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - William C. Surmeier
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Alexandria Melendez
- Department of Neurology, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Wokosin
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Tatiana Tkatch
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, Maryland, United States of America
| | - Vernon R. J. Clarke
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, Maryland, United States of America
| | - D. James Surmeier
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, Maryland, United States of America
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Boura-Halfon S, Haffner-Krausz R, Ben-Dor S, Kim JS, Jung S. Tackling Tissue Macrophage Heterogeneity by SplitCre Transgenesis. Methods Mol Biol 2024; 2713:481-503. [PMID: 37639143 DOI: 10.1007/978-1-0716-3437-0_32] [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
Macrophages represent a broad spectrum of distinct, but closely related tissue-resident immune cells. This presents a major challenge for the study of functional aspects of these cells using classical Cre recombinase-mediated conditional mutagenesis in mice, since single promoter-driven Cre transgenic models often display limited specificity toward their intended target. The advent of CRISPR/Cas9 technology has now provided a time- and cost-effective method to explore the full potential of binary transgenic, intersectional genetics. Specifically, the use of two promoters driving inactive Cre fragments that, when co-expressed, dimerize and only then gain recombinase activity allows the characterization and manipulation of genetically defined tissue macrophage subpopulations. Here, we will elaborate on the use of this protocol to capitalize on these recent technological advances in mouse genetics and discuss their strengths and pitfalls to improve the study of tissue macrophage subpopulations in physiology and pathophysiology.
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Affiliation(s)
- Sigalit Boura-Halfon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | | | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Jung-Seok Kim
- 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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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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Nava S, Palma W, Wan X, Oh JY, Gharib S, Wang H, Revanna JS, Tan M, Zhang M, Liu J, Chen CH, Lee JS, Perry B, Sternberg PW. A cGAL-UAS bipartite expression toolkit for Caenorhabditis elegans sensory neurons. Proc Natl Acad Sci U S A 2023; 120:e2221680120. [PMID: 38096407 PMCID: PMC10743456 DOI: 10.1073/pnas.2221680120] [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: 12/26/2022] [Accepted: 10/05/2023] [Indexed: 12/18/2023] Open
Abstract
Animals integrate sensory information from the environment and display various behaviors in response to external stimuli. In Caenorhabditis elegans hermaphrodites, 33 types of sensory neurons are responsible for chemosensation, olfaction, and mechanosensation. However, the functional roles of all sensory neurons have not been systematically studied due to the lack of facile genetic accessibility. A bipartite cGAL-UAS system has been previously developed to study tissue- or cell-specific functions in C. elegans. Here, we report a toolkit of new cGAL drivers that can facilitate the analysis of a vast majority of the 60 sensory neurons in C. elegans hermaphrodites. We generated 37 sensory neuronal cGAL drivers that drive cGAL expression by cell-specific regulatory sequences or intersection of two distinct regulatory regions with overlapping expression (split cGAL). Most cGAL-drivers exhibit expression in single types of cells. We also constructed 28 UAS effectors that allow expression of proteins to perturb or interrogate sensory neurons of choice. This cGAL-UAS sensory neuron toolkit provides a genetic platform to systematically study the functions of C. elegans sensory neurons.
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Affiliation(s)
- Stephanie Nava
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Wilber Palma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Xuan Wan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Jun Young Oh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Shahla Gharib
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Han Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Jasmin S. Revanna
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Minyi Tan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Mark Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Jonathan Liu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Chun-Hao Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - James S. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Barbara Perry
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - Paul W. Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
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Shaik SM, Cao Y, Gogola JV, Dodiya HB, Zhang X, Boutej H, Han W, Kriz J, Sisodia SS. Translational profiling identifies sex-specific metabolic and epigenetic reprogramming of cortical microglia/macrophages in APPPS1-21 mice with an antibiotic-perturbed-microbiome. Mol Neurodegener 2023; 18:95. [PMID: 38104136 PMCID: PMC10725591 DOI: 10.1186/s13024-023-00668-7] [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: 04/19/2023] [Accepted: 10/14/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Microglia, the brain-resident macrophages perform immune surveillance and engage with pathological processes resulting in phenotype changes necessary for maintaining homeostasis. In preceding studies, we showed that antibiotic-induced perturbations of the gut microbiome of APPPS1-21 mice resulted in significant attenuation in Aβ amyloidosis and altered microglial phenotypes that are specific to male mice. The molecular events underlying microglial phenotypic transitions remain unclear. Here, by generating 'APPPS1-21-CD11br' reporter mice, we investigated the translational state of microglial/macrophage ribosomes during their phenotypic transition and in a sex-specific manner. METHODS Six groups of mice that included WT-CD11br, antibiotic (ABX) or vehicle-treated APPPS1-21-CD11br males and females were sacrificed at 7-weeks of age (n = 15/group) and used for immunoprecipitation of microglial/macrophage polysomes from cortical homogenates using anti-FLAG antibody. Liquid chromatography coupled to tandem mass spectrometry and label-free quantification was used to identify newly synthesized peptides isolated from polysomes. RESULTS We show that ABX-treatment leads to decreased Aβ levels in male APPPS1-21-CD11br mice with no significant changes in females. We identified microglial/macrophage polypeptides involved in mitochondrial dysfunction and altered calcium signaling that are associated with Aβ-induced oxidative stress. Notably, female mice also showed downregulation of newly-synthesized ribosomal proteins. Furthermore, male mice showed an increase in newly-synthesized polypeptides involved in FcγR-mediated phagocytosis, while females showed an increase in newly-synthesized polypeptides responsible for actin organization associated with microglial activation. Next, we show that ABX-treatment resulted in substantial remodeling of the epigenetic landscape, leading to a metabolic shift that accommodates the increased bioenergetic and biosynthetic demands associated with microglial polarization in a sex-specific manner. While microglia in ABX-treated male mice exhibited a metabolic shift towards a neuroprotective phenotype that promotes Aβ clearance, microglia in ABX-treated female mice exhibited loss of energy homeostasis due to persistent mitochondrial dysfunction and impaired lysosomal clearance that was associated with inflammatory phenotypes. CONCLUSIONS Our studies provide the first snapshot of the translational state of microglial/macrophage cells in a mouse model of Aβ amyloidosis that was subject to ABX treatment. ABX-mediated changes resulted in metabolic reprogramming of microglial phenotypes to modulate immune responses and amyloid clearance in a sex-specific manner. This microglial plasticity to support neuro-energetic homeostasis for its function based on sex paves the path for therapeutic modulation of immunometabolism for neurodegeneration.
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Affiliation(s)
- Shabana M Shaik
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Yajun Cao
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Joseph V Gogola
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Hemraj B Dodiya
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Xulun Zhang
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Hejer Boutej
- CERVO Brain Research Centre and Department of Psychiatry and Neuroscience, Laval University, Québec, QC, Canada
| | - Weinong Han
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Jasna Kriz
- CERVO Brain Research Centre and Department of Psychiatry and Neuroscience, Laval University, Québec, QC, Canada
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Kellogg CM, Pham K, Ko S, Cox JE, Machalinski AH, Stout MB, Sharpe AL, Beckstead MJ, Chucair-Elliott AJ, Ocañas SR, Freeman WM. Specificity and efficiency of tamoxifen-mediated Cre induction is equivalent regardless of age. iScience 2023; 26:108413. [PMID: 38058312 PMCID: PMC10696116 DOI: 10.1016/j.isci.2023.108413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/15/2023] [Accepted: 11/02/2023] [Indexed: 12/08/2023] Open
Abstract
Temporally controlling Cre recombination through tamoxifen (Tam) induction has many advantages for biomedical research. Most studies report early post-natal/juvenile (<2 m.o.) Tam induction, but age-related neurodegeneration and aging studies can require Cre induction in older mice (>12 m.o.). While anecdotally reported as problematic, there are no published comparisons of Tam-mediated Cre induction at early and late ages. Here, microglial-specific Cx3cr1creERT2 mice were crossed to a floxed NuTRAP reporter to compare Cre induction at early (3-6 m.o.) and late (20 m.o.) ages. Specificity and efficiency of microglial labeling at 21-22 m.o. were identical in mice induced with Tam at early and late ages. Age-related microglial translatomic changes were also similar regardless of Tam induction age. Each Cre and flox mouse line should be independently validated, however, these findings demonstrate that Tam-mediated Cre induction can be performed even into older mouse ages and should be generalizable to other inducible Cre models.
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Affiliation(s)
- Collyn M. Kellogg
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kevin Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Sunghwan Ko
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jillian E.J. Cox
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Adeline H. Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Michael B. Stout
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Amanda L. Sharpe
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael J. Beckstead
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA
| | - Ana J. Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Sarah R. Ocañas
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M. Freeman
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA
- Neuroscience Graduate Program, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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Geibl FF, Henrich MT, Xie Z, Zampese E, Tkatch T, Wokosin DL, Nasiri E, Grotmann CA, Dawson VL, Dawson TM, Chandel NS, Oertel WH, Surmeier DJ. α-Synuclein pathology disrupts mitochondrial function in dopaminergic and cholinergic neurons at-risk in Parkinson's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571045. [PMID: 38168401 PMCID: PMC10759995 DOI: 10.1101/2023.12.11.571045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background Pathological accumulation of aggregated α-synuclein (aSYN) is a common feature of Parkinson's disease (PD). However, the mechanisms by which intracellular aSYN pathology contributes to dysfunction and degeneration of neurons in the brain are still unclear. A potentially relevant target of aSYN is the mitochondrion. To test this hypothesis, genetic and physiological methods were used to monitor mitochondrial function in substantia nigra pars compacta (SNc) dopaminergic and pedunculopontine nucleus (PPN) cholinergic neurons after stereotaxic injection of aSYN pre-formed fibrils (PFFs) into the mouse brain. Methods aSYN PPFs were stereotaxically injected into the SNc or PPN of mice. Twelve weeks later, mice were studied using a combination of approaches, including immunocytochemical analysis, cell- type specific transcriptomic profiling, electron microscopy, electrophysiology and two-photon-laser- scanning microscopy of genetically encoded sensors for bioenergetic and redox status. Results In addition to inducing a significant neuronal loss, SNc injection of PFFs induced the formation of intracellular, phosphorylated aSYN aggregates selectively in dopaminergic neurons. In these neurons, PFF-exposure decreased mitochondrial gene expression, reduced the number of mitochondria, increased oxidant stress, and profoundly disrupted mitochondrial adenosine triphosphate production. Consistent with an aSYN-induced bioenergetic deficit, the autonomous spiking of dopaminergic neurons slowed or stopped. PFFs also up-regulated lysosomal gene expression and increased lysosomal abundance, leading to the formation of Lewy-like inclusions. Similar changes were observed in PPN cholinergic neurons following aSYN PFF exposure. Conclusions Taken together, our findings suggest that disruption of mitochondrial function, and the subsequent bioenergetic deficit, is a proximal step in the cascade of events induced by aSYN pathology leading to dysfunction and degeneration of neurons at-risk in PD.
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Ugajin N, Imami K, Takada H, Ishihama Y, Chiba S, Mishima Y. Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development. RNA (NEW YORK, N.Y.) 2023; 29:1910-1927. [PMID: 37751929 PMCID: PMC10653392 DOI: 10.1261/rna.079633.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
The ribosome is a translational apparatus that comprises about 80 ribosomal proteins and four rRNAs. Recent studies reported that ribosome ubiquitination is crucial for translational regulation and ribosome-associated quality control (RQC). However, little is known about the dynamics of ribosome ubiquitination under complex biological processes of multicellular organisms. To explore ribosome ubiquitination during animal development, we generated a zebrafish strain that expresses a FLAG-tagged ribosomal protein Rpl36/eL36 from its endogenous locus. We examined ribosome ubiquitination during zebrafish development by combining affinity purification of ribosomes from rpl36-FLAG zebrafish embryos with immunoblotting analysis. Our findings showed that the ubiquitination of ribosomal proteins dynamically changed as development proceeded. We also showed that during zebrafish development, the ribosome was ubiquitinated by Znf598, an E3 ubiquitin ligase that activates RQC. Ribosomal protein Rps10/eS10 was found to be a key ubiquitinated protein during development. Furthermore, we showed that Rps10/eS10 ubiquitination-site mutations reduced the overall ubiquitination pattern of the ribosome. These results demonstrate the complexity and dynamics of ribosome ubiquitination during zebrafish development.
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Affiliation(s)
- Nozomi Ugajin
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Koshi Imami
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiraku Takada
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinobu Chiba
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yuichiro Mishima
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
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Forston MD, Wei GZ, Chariker JH, Stephenson T, Andres K, Glover C, Rouchka EC, Whittemore SR, Hetman M. Enhanced oxidative phosphorylation, re-organized intracellular signaling, and epigenetic de-silencing as revealed by oligodendrocyte translatome analysis after contusive spinal cord injury. Sci Rep 2023; 13:21254. [PMID: 38040794 PMCID: PMC10692148 DOI: 10.1038/s41598-023-48425-6] [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: 07/12/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
Reducing the loss of oligodendrocytes (OLs) is a major goal for neuroprotection after spinal cord injury (SCI). Therefore, the OL translatome was determined in Ribotag:Plp1-CreERT2 mice at 2, 10, and 42 days after moderate contusive T9 SCI. At 2 and 42 days, mitochondrial respiration- or actin cytoskeleton/cell junction/cell adhesion mRNAs were upregulated or downregulated, respectively. The latter effect suggests myelin sheath loss/morphological simplification which is consistent with downregulation of cholesterol biosynthesis transcripts on days 10 and 42. Various regulators of pro-survival-, cell death-, and/or oxidative stress response pathways showed peak expression acutely, on day 2. Many acutely upregulated OL genes are part of the repressive SUZ12/PRC2 operon suggesting that epigenetic de-silencing contributes to SCI effects on OL gene expression. Acute OL upregulation of the iron oxidoreductase Steap3 was confirmed at the protein level and replicated in cultured OLs treated with the mitochondrial uncoupler FCCP. Hence, STEAP3 upregulation may mark mitochondrial dysfunction. Taken together, in SCI-challenged OLs, acute and subchronic enhancement of mitochondrial respiration may be driven by axonal loss and subsequent myelin sheath degeneration. Acutely, the OL switch to oxidative phosphorylation may lead to oxidative stress that is further amplified by upregulation of such enzymes as STEAP3.
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Affiliation(s)
- Michael D Forston
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - George Z Wei
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- MD/PhD Program, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Julia H Chariker
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
- Neuroscience Training, University Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Tyler Stephenson
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Kariena Andres
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Charles Glover
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Eric C Rouchka
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Scott R Whittemore
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- MD/PhD Program, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Michal Hetman
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- MD/PhD Program, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
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Hu YX, Diao LT, Hou YR, Lv G, Tao S, Xu WY, Xie SJ, Ren YH, Xiao ZD. Pseudouridine synthase 1 promotes hepatocellular carcinoma through mRNA pseudouridylation to enhance the translation of oncogenic mRNAs. Hepatology 2023:01515467-990000000-00664. [PMID: 38015993 DOI: 10.1097/hep.0000000000000702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/10/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND AND AIMS Pseudouridine is a prevalent RNA modification and is highly present in the serum and urine of patients with HCC. However, the role of pseudouridylation and its modifiers in HCC remains unknown. We investigated the function and underlying mechanism of pseudouridine synthase 1 (PUS1) in HCC. APPROACH AND RESULTS By analyzing the TCGA data set, PUS1 was found to be significantly upregulated in human HCC specimens and positively correlated with tumor grade and poor prognosis of HCC. Knockdown of PUS1 inhibited cell proliferation and the growth of tumors in a subcutaneous xenograft mouse model. Accordingly, increased cell proliferation and tumor growth were observed in PUS1-overexpressing cells. Furthermore, overexpression of PUS1 significantly accelerates tumor formation in a mouse HCC model established by hydrodynamic tail vein injection, while knockout of PUS1 decreases it. Additionally, PUS1 catalytic activity is required for HCC tumorigenesis. Mechanistically, we profiled the mRNA targets of PUS1 by utilizing surveying targets by apolipoprotein B mRNA-editing enzyme 1 (APOBEC1)-mediated profiling and found that PUS1 incorporated pseudouridine into mRNAs of a set of oncogenes, thereby endowing them with greater translation capacity. CONCLUSIONS Our study highlights the critical role of PUS1 and pseudouridylation in HCC development, and provides new insight that PUS1 enhances the protein levels of a set of oncogenes, including insulin receptor substrate 1 (IRS1) and c-MYC, by means of pseudouridylation-mediated mRNA translation.
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Affiliation(s)
- Yan-Xia Hu
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Li-Ting Diao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Ya-Rui Hou
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Guo Lv
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Shuang Tao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Wan-Yi Xu
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Shu-Juan Xie
- Institute of Vaccine, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Ya-Han Ren
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Zhen-Dong Xiao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
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Gleichman AJ, Kawaguchi R, Sofroniew MV, Carmichael ST. A toolbox of astrocyte-specific, serotype-independent adeno-associated viral vectors using microRNA targeting sequences. Nat Commun 2023; 14:7426. [PMID: 37973910 PMCID: PMC10654773 DOI: 10.1038/s41467-023-42746-w] [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: 02/28/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023] Open
Abstract
Astrocytes, one of the most prevalent cell types in the central nervous system (CNS), are critically involved in neural function. Genetically manipulating astrocytes is an essential tool in understanding and affecting their roles. Adeno-associated viruses (AAVs) enable rapid genetic manipulation; however, astrocyte specificity of AAVs can be limited, with high off-target expression in neurons and sparsely in endothelial cells. Here, we report the development of a cassette of four copies of six miRNA targeting sequences (4x6T) which triggers transgene degradation specifically in neurons and endothelial cells. In combination with the GfaABC1D promoter, 4x6T increases astrocytic specificity of Cre with a viral reporter from <50% to >99% in multiple serotypes in mice, and confers astrocyte specificity in multiple recombinases and reporters. We also present empty vectors to add 4x6T to other cargo, independently and in Cre/Dre-dependent forms. This toolbox of AAVs allows rapid manipulation of astrocytes throughout the CNS, is compatible with different AAV serotypes, and demonstrates the efficacy of using multiplexed miRNA targeting sequences to decrease expression in multiple off-target cell populations simultaneously.
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Affiliation(s)
- Amy J Gleichman
- Department of Neurology, David Geffen School of Medicine at University of California-Los Angeles, Los Angeles, CA, USA
| | - Riki Kawaguchi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael V Sofroniew
- Department of Neurobiology, University of California-Los Angeles, Los Angeles, CA, USA
| | - S Thomas Carmichael
- Department of Neurology, David Geffen School of Medicine at University of California-Los Angeles, Los Angeles, CA, USA.
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Rajala RVS, Rajala A. Unlocking the role of lactate: metabolic pathways, signaling, and gene regulation in postmitotic retinal cells. FRONTIERS IN OPHTHALMOLOGY 2023; 3:1296624. [PMID: 38983010 PMCID: PMC11182115 DOI: 10.3389/fopht.2023.1296624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/19/2023] [Indexed: 07/11/2024]
Abstract
The Warburg effect, which was first described a century ago, asserts that mitotic tumor cells generate higher quantities of lactate. Intriguingly, even in typical physiological circumstances, postmitotic retinal photoreceptor cells also produce elevated levels of lactate. Initially classified as metabolic waste, lactate has since gained recognition as a significant intracellular signaling mediator and extracellular ligand. This current review endeavors to provide a concise overview and discourse on the following topics: the localization of lactate-producing enzymes, the functional significance of these enzymes, the signaling functions of lactate, and its impact on the gene expression of photoreceptors in retinal cells.
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Affiliation(s)
- Raju V. S. Rajala
- Departments of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Departments of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Departments of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Dean McGee Eye Institute, Oklahoma City, OK, United States
| | - Ammaji Rajala
- Departments of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Dean McGee Eye Institute, Oklahoma City, OK, United States
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Wong C, Tavares-Ferreira D, Thörn Perez C, Sharif B, Uttam S, Amiri M, Lister KC, Hooshmandi M, Nguyen V, Séguéla P, Sonenberg N, Price TJ, Gkogkas CG, Khoutorsky A. 4E-BP1-dependent translation in nociceptors controls mechanical hypersensitivity via TRIM32/type I interferon signaling. SCIENCE ADVANCES 2023; 9:eadh9603. [PMID: 37922363 PMCID: PMC10624345 DOI: 10.1126/sciadv.adh9603] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 10/03/2023] [Indexed: 11/05/2023]
Abstract
Activation of the mechanistic target of rapamycin complex 1 (mTORC1) contributes to the development of chronic pain. However, the specific mechanisms by which mTORC1 causes hypersensitivity remain elusive. The eukaryotic initiation factor 4E-binding protein 1 (4E-BP1) is a key mTORC1 downstream effector that represses translation initiation. Here, we show that nociceptor-specific deletion of 4E-BP1, mimicking activation of mTORC1-dependent translation, is sufficient to cause mechanical hypersensitivity. Using translating ribosome affinity purification in nociceptors lacking 4E-BP1, we identified a pronounced translational up-regulation of tripartite motif-containing protein 32 (TRIM32), an E3 ubiquitin ligase that promotes interferon signaling. Down-regulation of TRIM32 in nociceptors or blocking type I interferon signaling reversed the mechanical hypersensitivity in mice lacking 4E-BP1. Furthermore, nociceptor-specific ablation of TRIM32 alleviated mechanical hypersensitivity caused by tissue inflammation. These results show that mTORC1 in nociceptors promotes hypersensitivity via 4E-BP1-dependent up-regulation of TRIM32/interferon signaling and identify TRIM32 as a therapeutic target in inflammatory pain.
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Affiliation(s)
- Calvin Wong
- Department of Anaesthesia, McGill University, Montreal, Canada
| | - Diana Tavares-Ferreira
- School of Behavioural and Brain Sciences and Center for Advanced Pain Studies, University of Texas at Dallas, Dallas, TX 75080, USA
| | - Carolina Thörn Perez
- Department of Anaesthesia, McGill University, Montreal, Canada
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Behrang Sharif
- Department of Physiology, McGill University, Montreal, Canada
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Sonali Uttam
- Department of Anaesthesia, McGill University, Montreal, Canada
| | - Mehdi Amiri
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Canada
- Department of Biochemistry, McGill University, Montreal, Canada
| | - Kevin C. Lister
- Department of Anaesthesia, McGill University, Montreal, Canada
| | | | - Vivienne Nguyen
- Department of Anaesthesia, McGill University, Montreal, Canada
| | - Philippe Séguéla
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - Nahum Sonenberg
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Canada
- Department of Biochemistry, McGill University, Montreal, Canada
| | - Theodore J. Price
- School of Behavioural and Brain Sciences and Center for Advanced Pain Studies, University of Texas at Dallas, Dallas, TX 75080, USA
| | - Christos G. Gkogkas
- Biomedical Research Institute, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Arkady Khoutorsky
- Department of Anaesthesia, McGill University, Montreal, Canada
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Canada
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Itoh N, Itoh Y, Stiles L, Voskuhl R. Sex differences in the neuronal transcriptome and synaptic mitochondrial function in the cerebral cortex of a multiple sclerosis model. Front Neurol 2023; 14:1268411. [PMID: 38020654 PMCID: PMC10654219 DOI: 10.3389/fneur.2023.1268411] [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: 07/28/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Multiple sclerosis (MS) affects the cerebral cortex, inducing cortical atrophy and neuronal and synaptic pathology. Despite the fact that women are more susceptible to getting MS, men with MS have worse disability progression. Here, sex differences in neurodegenerative mechanisms are determined in the cerebral cortex using the MS model, chronic experimental autoimmune encephalomyelitis (EAE). Methods Neurons from cerebral cortex tissues of chronic EAE, as well as age-matched healthy control, male and female mice underwent RNA sequencing and gene expression analyses using RiboTag technology. The morphology of mitochondria in neurons of cerebral cortex was assessed using Thy1-CFP-MitoS mice. Oxygen consumption rates were determined using mitochondrial respirometry assays from intact as well as permeabilized synaptosomes. Results RNA sequencing of neurons in cerebral cortex during chronic EAE in C57BL/6 mice showed robust differential gene expression in male EAE compared to male healthy controls. In contrast, there were few differences in female EAE compared to female healthy controls. The most enriched differential gene expression pathways in male mice during EAE were mitochondrial dysfunction and oxidative phosphorylation. Mitochondrial morphology in neurons showed significant abnormalities in the cerebral cortex of EAE males, but not EAE females. Regarding function, synaptosomes isolated from cerebral cortex of male, but not female, EAE mice demonstrated significantly decreased oxygen consumption rates during respirometry assays. Discussion Cortical neuronal transcriptomics, mitochondrial morphology, and functional respirometry assays in synaptosomes revealed worse neurodegeneration in male EAE mice. This is consistent with worse neurodegeneration in MS men and reveals a model and a target to develop treatments to prevent cortical neurodegeneration and mitigate disability progression in MS men.
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Affiliation(s)
- Noriko Itoh
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Yuichiro Itoh
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Linsey Stiles
- Department of Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Rhonda Voskuhl
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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Cagnetta R, Flanagan JG, Sonenberg N. Control of Selective mRNA Translation in Neuronal Subcellular Compartments in Health and Disease. J Neurosci 2023; 43:7247-7263. [PMID: 37914402 PMCID: PMC10621772 DOI: 10.1523/jneurosci.2240-22.2023] [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: 12/06/2022] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 11/03/2023] Open
Abstract
In multiple cell types, mRNAs are transported to subcellular compartments, where local translation enables rapid, spatially localized, and specific responses to external stimuli. Mounting evidence has uncovered important roles played by local translation in vivo in axon survival, axon regeneration, and neural wiring, as well as strong links between dysregulation of local translation and neurologic disorders. Omic studies have revealed that >1000 mRNAs are present and can be selectively locally translated in the presynaptic and postsynaptic compartments from development to adulthood in vivo A large proportion of the locally translated mRNAs is specifically upregulated or downregulated in response to distinct extracellular signals. Given that the local translatome is large, selectively translated, and cue-specifically remodeled, a fundamental question concerns how selective translation is achieved locally. Here, we review the emerging regulatory mechanisms of local selective translation in neuronal subcellular compartments, their mRNA targets, and their orchestration. We discuss mechanisms of local selective translation that remain unexplored. Finally, we describe clinical implications and potential therapeutic strategies in light of the latest advances in gene therapy.
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Affiliation(s)
- Roberta Cagnetta
- Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - John G Flanagan
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, Massachusetts 02115
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal, Quebec H3A 1A3, Canada
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Tubert C, Zampese E, Pancani T, Tkatch T, Surmeier DJ. Feed-forward metabotropic signaling by Cav1 Ca 2+ channels supports pacemaking in pedunculopontine cholinergic neurons. Neurobiol Dis 2023; 188:106328. [PMID: 37852390 PMCID: PMC10792542 DOI: 10.1016/j.nbd.2023.106328] [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: 08/04/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/20/2023] Open
Abstract
Like a handful of other neuronal types in the brain, cholinergic neurons (CNs) in the pedunculopontine nucleus (PPN) are lost during Parkinson's disease (PD). Why this is the case is unknown. One neuronal trait implicated in PD selective neuronal vulnerability is the engagement of feed-forward stimulation of mitochondrial oxidative phosphorylation (OXPHOS) to meet high bioenergetic demand, leading to sustained oxidant stress and ultimately degeneration. The extent to which this trait is shared by PPN CNs is unresolved. To address this question, a combination of molecular and physiological approaches were used. These studies revealed that PPN CNs are autonomous pacemakers with modest spike-associated cytosolic Ca2+ transients. These Ca2+ transients were partly attributable to the opening of high-threshold Cav1.2 Ca2+ channels, but not Cav1.3 channels. Cav1.2 channel signaling through endoplasmic reticulum ryanodine receptors stimulated mitochondrial OXPHOS to help maintain cytosolic adenosine triphosphate (ATP) levels necessary for pacemaking. Inhibition of Cav1.2 channels led to the recruitment of ATP-sensitive K+ channels and the slowing of pacemaking. A 'side-effect' of Cav1.2 channel-mediated stimulation of mitochondria was increased oxidant stress. Thus, PPN CNs have a distinctive physiological phenotype that shares some, but not all, of the features of other neurons that are selectively vulnerable in PD.
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Affiliation(s)
- C Tubert
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Universidad de Buenos Aires - CONICET. Instituto de Fisiología y Biofísica Bernardo Houssay (IFIBIO Houssay), Facultad de Medicina, Departamento de Ciencias Fisiológicas, Grupo de Neurociencia de Sistemas, Buenos Aires, Argentina
| | - E Zampese
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - T Pancani
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL 33458, USA
| | - T Tkatch
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - D J Surmeier
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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Kim YT, Park BS, Yang HR, Yi S, Nam-Goong IS, Kim JG. Exploring the potential hypothalamic role in mediating cisplatin-induced negative energy balance. Chem Biol Interact 2023; 385:110733. [PMID: 37769865 DOI: 10.1016/j.cbi.2023.110733] [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: 07/14/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Cisplatin is a chemotherapeutic drug commonly used for treating different types of cancer. However, long-term use can lead to side effects, including anorexia, nausea, vomiting, and weight loss, which negatively affect the patient's quality of life and ability to undergo chemotherapy. This study aimed to investigate the mechanisms underlying the development of a negative energy balance during cisplatin treatment. Mice treated with cisplatin exhibit reduced food intake, body weight, and energy expenditure. We observed altered neuronal activity in the hypothalamic nuclei involved in the regulation of energy metabolism in cisplatin-treated mice. In addition, we observed activation of microglia and inflammation in the hypothalamus following treatment with cisplatin. Consistent with this finding, inhibition of microglial activation effectively rescued cisplatin-induced anorexia and body weight loss. The present study identified the role of hypothalamic neurons and inflammation linked to microglial activation in the anorexia and body weight loss observed during cisplatin treatment. These findings provide insight into the mechanisms underlying the development of metabolic abnormalities during cisplatin treatment and suggest new strategies for managing these side effects.
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Affiliation(s)
- Yang Tae Kim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Byong Seo Park
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Hye Rim Yang
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Seon Yi
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Il Seong Nam-Goong
- Department of Internal Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, 682-714, Republic of Korea.
| | - Jae Geun Kim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea; Research Center of Brain-Machine Interface, Incheon National University, Incheon, 22012, Republic of Korea.
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Clarkson BD, Grund EM, Standiford MM, Mirchia K, Westphal MS, Muschler LS, Howe CL. CD8+ T cells recognizing a neuron-restricted antigen injure axons in a model of multiple sclerosis. J Clin Invest 2023; 133:e162788. [PMID: 37676734 PMCID: PMC10617772 DOI: 10.1172/jci162788] [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: 06/16/2022] [Accepted: 09/06/2023] [Indexed: 09/09/2023] Open
Abstract
CD8+ T cells outnumber CD4+ cells in multiple sclerosis (MS) lesions associated with disease progression, but the pathogenic role and antigenic targets of these clonally expanded effectors are unknown. Based on evidence that demyelination is necessary but not sufficient for disease progression in MS, we previously hypothesized that CNS-infiltrating CD8+ T cells specific for neuronal antigens directly drive the axonal and neuronal injury that leads to cumulative neurologic disability in patients with MS. We now show that demyelination induced expression of MHC class I on neurons and axons and resulted in presentation of a neuron-specific neoantigen (synapsin promoter-driven chicken ovalbumin) to antigen-specific CD8+ T cells (anti-ovalbumin OT-I TCR-transgenic T cells). These neuroantigen-specific effectors surveilled the CNS in the absence of demyelination but were not retained. However, upon induction of demyelination via cuprizone intoxication, neuroantigen-specific CD8+ T cells proliferated, accumulated in the CNS, and damaged neoantigen-expressing neurons and axons. We further report elevated neuronal expression of MHC class I and β2-microglobulin transcripts and protein in gray matter and white matter tracts in tissue from patients with MS. These findings support a pathogenic role for autoreactive anti-axonal and anti-neuronal CD8+ T cells in MS progression.
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Affiliation(s)
- Benjamin D.S. Clarkson
- Department of Neurology
- Department of Laboratory Medicine and Pathology
- Center for Multiple Sclerosis and Autoimmune Neurology
| | | | | | | | | | | | - Charles L. Howe
- Department of Neurology
- Center for Multiple Sclerosis and Autoimmune Neurology
- Division of Experimental Neurology, Mayo Clinic, Rochester, Minnesota, USA
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