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Sertbas M, Ulgen KO. Exploring Human Brain Metabolism via Genome-Scale Metabolic Modeling with Highlights on Multiple Sclerosis. ACS Chem Neurosci 2025; 16:1346-1360. [PMID: 40091499 PMCID: PMC11969529 DOI: 10.1021/acschemneuro.5c00006] [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: 01/06/2025] [Revised: 02/18/2025] [Accepted: 03/03/2025] [Indexed: 03/19/2025] Open
Abstract
Cerebral dysfunctions give rise to a wide range of neurological diseases due to the structural and functional complexity of the human brain stemming from the interactive cellular metabolism of its specific cells, including neurons and glial cells. In parallel with advances in isolation and measurement technologies, genome-scale metabolic models (GEMs) have become a powerful tool in the studies of systems biology to provide critical insights into the understanding of sophisticated eukaryotic systems. In this study, brain cell-specific GEMs were reconstructed for neurons, astrocytes, microglia, oligodendrocytes, and oligodendrocyte precursor cells by integrating single-cell RNA-seq data and global Human1 via a task-driven integrative network inference for tissues (tINIT) algorithm. Then, intercellular reactions among neurons, astrocytes, microglia, and oligodendrocytes were added to generate a combined brain model, iHumanBrain2690. This brain network was used in the prediction of metabolic alterations in glucose, ketone bodies, oxygen change, and reporter metabolites. Glucose supplementation increased the subsystems' activities in glycolysis, and ketone bodies elevated those in the TCA cycle and oxidative phosphorylation. Reporter metabolite analysis identified L-carnitine and arachidonate as the top reporter metabolites in gray and white matter microglia in multiple sclerosis (MS), respectively. Carbamoyl-phosphate was found to be the top reporter metabolite in primary progressive MS. Taken together, single and integrated iHumanBrain2690 metabolic networks help us elucidate complex metabolism in brain physiology and homeostasis in health and disease.
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Affiliation(s)
- Mustafa Sertbas
- Department
of Chemical Engineering, Bogazici University, 34342 Istanbul, Turkey
- Department
of Chemical Engineering, Istanbul Technical
University, 34469 Istanbul, Turkey
| | - Kutlu O. Ulgen
- Department
of Chemical Engineering, Bogazici University, 34342 Istanbul, Turkey
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2
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Liu N, Jiang Y, Xiu Y, Tortelote GG, Xia W, Wang Y, Li Y, Shi S, Han J, Vidoudez C, Niamnud A, Kilgore MD, Zhou D, Shi M, Graziose SA, Fan J, Katakam PVG, Dumont AS, Wang X. Itaconate restrains acute proinflammatory activation of microglia after traumatic brain injury in mice. Sci Transl Med 2025; 17:eadn2635. [PMID: 40073156 DOI: 10.1126/scitranslmed.adn2635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 08/18/2024] [Accepted: 02/13/2025] [Indexed: 03/14/2025]
Abstract
Traumatic brain injury (TBI) rapidly triggers proinflammatory activation of microglia, contributing to secondary brain damage post-TBI. Although the governing role of energy metabolism in shaping the inflammatory phenotype and function of immune cells has been increasingly recognized, the specific alterations in microglial bioenergetics post-TBI remain poorly understood. Itaconate, a metabolite produced by the enzyme aconitate decarboxylase 1 [IRG1; encoded by immune responsive gene 1 (Irg1)], is a pivotal metabolic regulator in immune cells, particularly in macrophages. Because microglia are macrophages of the brain parenchyma, the IRG1/itaconate pathway likely modulates microglial inflammatory responses. In this study, we explored the role of the IRG1/itaconate pathway in regulating microglial bioenergetics and inflammatory activation post-TBI using a mouse controlled cortical impact (CCI) model. We isolated microglia before and 4 and 12 hours after TBI and observed a swift but transient increase in glycolysis coupled with a prolonged disruption of mitochondrial metabolism after injury. Despite an up-regulation of Irg1 expression, itaconate in microglia declined after TBI. Microglia-specific Irg1 gene knockout (Irg1-Mi-KO) exacerbated metabolic changes, intensified proinflammatory activation and neurodegeneration, and worsened certain long-term neurological deficits. Supplementation with 4-octyl itaconate (OI) reinstated the use and oxidative metabolism of glucose, glutamine, and fatty acid, thereby enhancing microglial bioenergetics post-TBI. OI supplementation also attenuated proinflammatory activation and neurodegeneration and improved long-term neurological outcomes. These results suggest that therapeutically targeting the itaconate pathway could improve microglial energy metabolism and neurological outcomes after TBI.
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Affiliation(s)
- Ning Liu
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane University Translational Sciences Institute, New Orleans, LA 70112, USA
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, LA 70112, USA
| | - Yinghua Jiang
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Yuwen Xiu
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Giovane G Tortelote
- Department of Pediatrics and Tulane Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Winna Xia
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Yingjie Wang
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Yadan Li
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Samuel Shi
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jinrui Han
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Charles Vidoudez
- Harvard Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Aim Niamnud
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Mitchell D Kilgore
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Di Zhou
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Mengxuan Shi
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Stephen A Graziose
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jia Fan
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Prasad V G Katakam
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, LA 70112, USA
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Aaron S Dumont
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Xiaoying Wang
- Clinical Neuroscience Research Center, Department of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, LA 70112, USA
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3
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Bielanin JP, Sun D. Significance of Microglial Energy Metabolism in Maintaining Brain Homeostasis. Transl Stroke Res 2023; 14:435-437. [PMID: 35879639 PMCID: PMC9877240 DOI: 10.1007/s12975-022-01069-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 01/29/2023]
Affiliation(s)
- John P Bielanin
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Pittsburgh Institute for Neurodegenerative Disorders, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Dandan Sun
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
- Pittsburgh Institute for Neurodegenerative Disorders, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
- Veterans Affairs Pittsburgh Health Care System, Pittsburgh, PA, 15213, USA.
- Department of Neurology, University of Pittsburgh Medical School, 7016 Biomedical Science Tower-3, 3501 Fifth Ave., Pittsburgh, PA, 15260, USA.
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Establishment and Application of a Novel In Vitro Model of Microglial Activation in Traumatic Brain Injury. J Neurosci 2023; 43:319-332. [PMID: 36446585 PMCID: PMC9838700 DOI: 10.1523/jneurosci.1539-22.2022] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Mechanical impact-induced primary injury after traumatic brain injury (TBI) leads to acute microglial pro-inflammatory activation and consequently mediates neurodegeneration, which is a major secondary brain injury mechanism. However, the detailed pathologic cascades have not been fully elucidated, partially because of the pathologic complexity in animal TBI models. Although there are several in vitro TBI models, none of them closely mimic post-TBI microglial activation. In the present study, we aimed to establish an in vitro TBI model, specifically reconstituting the pro-inflammatory activation and associated neurodegeneration following TBI. We proposed three sets of experiments. First, we established a needle scratch injured neuron-induced microglial activation and neurodegeneration in vitro model of TBI. Second, we compared microglial pro-inflammatory cytokines profiles between the in vitro TBI model and TBI in male mice. Additionally, we validated the role of injured neurons-derived damage-associated molecular patterns in amplifying microglial pro-inflammatory pathways using the in vitro TBI model. Third, we applied the in vitro model for the first time to characterize the cellular metabolic profile of needle scratch injured-neuron-activated microglia, and define the role of metabolic reprogramming in mediating pro-inflammatory microglial activation and mediated neurodegeneration. Our results showed that we successfully established a novel in vitro TBI model, which closely mimics primary neuronal injury-triggered microglial pro-inflammatory activation and mediated neurodegeneration after TBI. This in vitro model provides an advanced and highly translational platform for dissecting interactions in the pathologic processes of neuronal injury-microglial activation-neuronal degeneration cascade, and elucidating the detailed underlying cellular and molecular insights after TBI.SIGNIFICANCE STATEMENT Microglial activation is a key component of acute neuroinflammation that leads to neurodegeneration and long-term neurologic outcome deficits after TBI. However, it is not feasible to truly dissect primary neuronal injury-induced microglia activation, and consequently mediated neurodegeneration in vivo Furthermore, there is currently lacking of in vitro TBI models closely mimicking the TBI primary injury-mediated microglial activation. In this study, we successfully established and validated a novel in vitro TBI model of microglial activation, and for the first time, characterized the cellular metabolic profile of microglia in this model. This novel microglial activation in vitro TBI model will help in elucidating microglial inflammatory activation and consequently associated neurodegeneration after TBI.
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Zeng J, Bao T, Yang K, Zhu X, Wang S, Xiang W, Ge A, Zeng L, Ge J. The mechanism of microglia-mediated immune inflammation in ischemic stroke and the role of natural botanical components in regulating microglia: A review. Front Immunol 2022; 13:1047550. [PMID: 36818470 PMCID: PMC9933144 DOI: 10.3389/fimmu.2022.1047550] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 12/05/2022] [Indexed: 02/05/2023] Open
Abstract
Ischemic stroke (IS) is one of the most fatal diseases. Neuroimmunity, inflammation, and oxidative stress play important roles in various complex mechanisms of IS. In particular, the early proinflammatory response resulting from the overactivation of resident microglia and the infiltration of circulating monocytes and macrophages in the brain after cerebral ischemia leads to secondary brain injury. Microglia are innate immune cells in the brain that constantly monitor the brain microenvironment under normal conditions. Once ischemia occurs, microglia are activated to produce dual effects of neurotoxicity and neuroprotection, and the balance of the two effects determines the fate of damaged neurons. The activation of microglia is defined as the classical activation (M1 type) or alternative activation (M2 type). M1 type microglia secrete pro-inflammatory cytokines and neurotoxic mediators to exacerbate neuronal damage, while M2 type microglia promote a repairing anti-inflammatory response. Fine regulation of M1/M2 microglial activation to minimize damage and maximize protection has important therapeutic value. This review focuses on the interaction between M1/M2 microglia and other immune cells involved in the regulation of IS phenotypic characteristics, and the mechanism of natural plant components regulating microglia after IS, providing novel candidate drugs for regulating microglial balance and IS drug development.
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Affiliation(s)
- Jinsong Zeng
- The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Tingting Bao
- Institute of Metabolic Diseases, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Kailin Yang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | | | - Shanshan Wang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Wang Xiang
- Department of Rheumatology, The First People's Hospital Changde City, Changde, Hunan, China
| | - Anqi Ge
- The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Liuting Zeng
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Jinwen Ge
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China.,Hunan Academy of Chinese Medicine, Changsha, Hunan, China
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Ashwal S, Siebold L, Krueger AC, Wilson CG. Post-traumatic Neuroinflammation: Relevance to Pediatrics. Pediatr Neurol 2021; 122:50-58. [PMID: 34304972 DOI: 10.1016/j.pediatrneurol.2021.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
Both detrimental and beneficial effects of post-traumatic neuroinflammation have become a major research focus as they offer the potential for immediate as well as delayed targeted reparative therapies. Understanding the complex interactions of central and peripheral immunocompetent cells as well as their mediators on brain injury and recovery is complicated by the temporal, regional, and developmental differences in their response to injuries. Microglia, the brain-resident macrophages, have become central in these investigations as they serve a major surveillance function, have the ability to react swiftly to injury, recruit various cellular and chemical mediators, and monitor the reparative/degenerative processes. In this review we describe selected aspects of this burgeoning literature, describing the critical role of cytokines and chemokines, microglia, advances in neuroimaging, genetics and fractal morphology analysis, our research efforts in this area, and selected aspects of pediatric post-traumatic neuroinflammation.
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Affiliation(s)
- Stephen Ashwal
- Department of Pediatrics, Loma Linda University, School of Medicine, Loma Linda, California.
| | - Lorraine Siebold
- Department of Pediatrics, Loma Linda University, School of Medicine, Loma Linda, California
| | - A Camille Krueger
- Department of Pediatrics, Loma Linda University, School of Medicine, Loma Linda, California
| | - Christopher G Wilson
- Department of Pediatrics, Loma Linda University, School of Medicine, Loma Linda, California
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