1
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Ozgür-Gunes Y, Le Stunff C, Bougnères P. Oligodendrocytes, the Forgotten Target of Gene Therapy. Cells 2024; 13:1973. [PMID: 39682723 DOI: 10.3390/cells13231973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Revised: 11/22/2024] [Accepted: 11/26/2024] [Indexed: 12/18/2024] Open
Abstract
If the billions of oligodendrocytes (OLs) populating the central nervous system (CNS) of patients could express their feelings, they would undoubtedly tell gene therapists about their frustration with the other neural cell populations, neurons, microglia, or astrocytes, which have been the favorite targets of gene transfer experiments. This review questions why OLs have been left out of most gene therapy attempts. The first explanation is that the pathogenic role of OLs is still discussed in most CNS diseases. Another reason is that the so-called ubiquitous CAG, CBA, CBh, or CMV promoters-widely used in gene therapy studies-are unable or poorly able to activate the transcription of episomal transgene copies brought by adeno-associated virus (AAV) vectors in OLs. Accordingly, transgene expression in OLs has either not been found or not been evaluated in most gene therapy studies in rodents or non-human primates. The aims of the current review are to give OLs their rightful place among the neural cells that future gene therapy could target and to encourage researchers to test the effect of OL transduction in various CNS diseases.
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Affiliation(s)
- Yasemin Ozgür-Gunes
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Catherine Le Stunff
- MIRCen Institute, Laboratoire des Maladies Neurodégénératives, Commissariat à l'Energie Atomique, 92260 Fontenay-aux-Roses, France
- NEURATRIS at MIRCen, 92260 Fontenay-aux-Roses, France
- UMR1195 Inserm and University Paris Saclay, 94270 Le Kremlin-Bicêtre, France
| | - Pierre Bougnères
- MIRCen Institute, Laboratoire des Maladies Neurodégénératives, Commissariat à l'Energie Atomique, 92260 Fontenay-aux-Roses, France
- NEURATRIS at MIRCen, 92260 Fontenay-aux-Roses, France
- Therapy Design Consulting, 94300 Vincennes, France
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2
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Perdaens O, van Pesch V. Should We Consider Neurodegeneration by Itself or in a Triangulation with Neuroinflammation and Demyelination? The Example of Multiple Sclerosis and Beyond. Int J Mol Sci 2024; 25:12637. [PMID: 39684351 DOI: 10.3390/ijms252312637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 11/20/2024] [Accepted: 11/20/2024] [Indexed: 12/18/2024] Open
Abstract
Neurodegeneration is preeminent in many neurological diseases, and still a major burden we fail to manage in patient's care. Its pathogenesis is complicated, intricate, and far from being completely understood. Taking multiple sclerosis as an example, we propose that neurodegeneration is neither a cause nor a consequence by itself. Mitochondrial dysfunction, leading to energy deficiency and ion imbalance, plays a key role in neurodegeneration, and is partly caused by the oxidative stress generated by microglia and astrocytes. Nodal and paranodal disruption, with or without myelin alteration, is further involved. Myelin loss exposes the axons directly to the inflammatory and oxidative environment. Moreover, oligodendrocytes provide a singular metabolic and trophic support to axons, but do not emerge unscathed from the pathological events, by primary myelin defects and cell apoptosis or secondary to neuroinflammation or axonal damage. Hereby, trophic failure might be an overlooked contributor to neurodegeneration. Thus, a complex interplay between neuroinflammation, demyelination, and neurodegeneration, wherein each is primarily and secondarily involved, might offer a more comprehensive understanding of the pathogenesis and help establishing novel therapeutic strategies for many neurological diseases and beyond.
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Affiliation(s)
- Océane Perdaens
- Neurochemistry Group, Institute of NeuroScience, Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Vincent van Pesch
- Neurochemistry Group, Institute of NeuroScience, Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
- Department of Neurology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
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3
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Zhang FL, Li AY, Niu YL, Zhang K, Zhao MH, Huang JJ, Shen W. Identification of biomarkers in Parkinson's disease by comparative transcriptome analysis and WGCNA highlights the role of oligodendrocyte precursor cells. Front Aging Neurosci 2024; 16:1485722. [PMID: 39634657 PMCID: PMC11615075 DOI: 10.3389/fnagi.2024.1485722] [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: 08/24/2024] [Accepted: 11/07/2024] [Indexed: 12/07/2024] Open
Abstract
Background Parkinson's disease (PD) is an age-related neurodegenerative disease characterized by the death of dopamine neurons in the substantia nigra. A large number of studies have focused on dopamine neurons themselves, but so far, the pathogenesis of PD has not been fully elucidated. Results Here, we explored the significance of oligodendrocyte precursor cells (OPCs)/oligodendrocytes in the pathogenesis of PD using a bioinformatic approach. WGCNA analysis suggested that abnormal development of oligodendrocytes may play a key role in early PD. To verify the transcriptional dynamics of OPCs/oligodendrocytes, we performed differential analysis, cell trajectory construction, cell communication analysis and hdWGCNA analysis using single-cell data from PD patients. Interestingly, the results indicated that there was overlap between hub genes and differentially expressed genes (DEGs) in OPCs not in oligodendrocytes, suggesting that OPCs may be more sensitive to PD drivers. Then, we used ROC binary analysis model to identify five potential biomarkers, including AGPAT4, DNM3, PPP1R12B, PPP2R2B, and LINC00486. Conclusion In conclusion, our work highlights the potential role of OPCs in driving PD.
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Affiliation(s)
- Fa-Li Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Ai-Ying Li
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yi-Lin Niu
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Kai Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Ming-Hui Zhao
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jiao-Jiao Huang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Wei Shen
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
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4
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Miller MR, Landis HE, Miller RE, Tizabi Y. Intercellular Adhesion Molecule 1 (ICAM-1): An Inflammatory Regulator with Potential Implications in Ferroptosis and Parkinson's Disease. Cells 2024; 13:1554. [PMID: 39329738 PMCID: PMC11430830 DOI: 10.3390/cells13181554] [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: 08/09/2024] [Revised: 09/09/2024] [Accepted: 09/13/2024] [Indexed: 09/28/2024] Open
Abstract
Intercellular adhesion molecule 1 (ICAM-1/CD54), a transmembrane glycoprotein, has been considered as one of the most important adhesion molecules during leukocyte recruitment. It is encoded by the ICAM1 gene and plays a central role in inflammation. Its crucial role in many inflammatory diseases such as ulcerative colitis and rheumatoid arthritis are well established. Given that neuroinflammation, underscored by microglial activation, is a key element in neurodegenerative diseases such as Parkinson's disease (PD), we investigated whether ICAM-1 has a role in this progressive neurological condition and, if so, to elucidate the underpinning mechanisms. Specifically, we were interested in the potential interaction between ICAM-1, glial cells, and ferroptosis, an iron-dependent form of cell death that has recently been implicated in PD. We conclude that there exist direct and indirect (via glial cells and T cells) influences of ICAM-1 on ferroptosis and that further elucidation of these interactions can suggest novel intervention for this devastating disease.
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Affiliation(s)
| | - Harold E. Landis
- Integrative Medicine Fellow, University of Arizona College of Medicine, Tucson, AZ 85724, USA
| | | | - Yousef Tizabi
- Department of Pharmacology, Howard University College of Medicine, 520 W Street NW, Washington, DC 20059, USA
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5
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Hoang N, Sardaripour N, Ramey GD, Schilling K, Liao E, Chen Y, Park JH, Bledsoe X, Landman BA, Gamazon ER, Benton ML, Capra JA, Rubinov M. Integration of estimated regional gene expression with neuroimaging and clinical phenotypes at biobank scale. PLoS Biol 2024; 22:e3002782. [PMID: 39269986 PMCID: PMC11424006 DOI: 10.1371/journal.pbio.3002782] [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: 03/22/2024] [Revised: 09/25/2024] [Accepted: 08/01/2024] [Indexed: 09/15/2024] Open
Abstract
An understanding of human brain individuality requires the integration of data on brain organization across people and brain regions, molecular and systems scales, as well as healthy and clinical states. Here, we help advance this understanding by leveraging methods from computational genomics to integrate large-scale genomic, transcriptomic, neuroimaging, and electronic-health record data sets. We estimated genetically regulated gene expression (gr-expression) of 18,647 genes, across 10 cortical and subcortical regions of 45,549 people from the UK Biobank. First, we showed that patterns of estimated gr-expression reflect known genetic-ancestry relationships, regional identities, as well as inter-regional correlation structure of directly assayed gene expression. Second, we performed transcriptome-wide association studies (TWAS) to discover 1,065 associations between individual variation in gr-expression and gray-matter volumes across people and brain regions. We benchmarked these associations against results from genome-wide association studies (GWAS) of the same sample and found hundreds of novel associations relative to these GWAS. Third, we integrated our results with clinical associations of gr-expression from the Vanderbilt Biobank. This integration allowed us to link genes, via gr-expression, to neuroimaging and clinical phenotypes. Fourth, we identified associations of polygenic gr-expression with structural and functional MRI phenotypes in the Human Connectome Project (HCP), a small neuroimaging-genomic data set with high-quality functional imaging data. Finally, we showed that estimates of gr-expression and magnitudes of TWAS were generally replicable and that the p-values of TWAS were replicable in large samples. Collectively, our results provide a powerful new resource for integrating gr-expression with population genetics of brain organization and disease.
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Affiliation(s)
- Nhung Hoang
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Neda Sardaripour
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Grace D. Ramey
- Biological and Medical Informatics Division, University of California, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, United States of America
| | - Kurt Schilling
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Emily Liao
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Yiting Chen
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jee Hyun Park
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Xavier Bledsoe
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Bennett A. Landman
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Eric R. Gamazon
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Mary Lauren Benton
- Department of Computer Science, Baylor University, Waco, Texas, United States of America
| | - John A. Capra
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Bakar Computational Health Sciences Institute, University of California, San Francisco, California, United States of America
| | - Mikail Rubinov
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Psychology, Vanderbilt University, Nashville, Tennessee, United States of America
- Howard Hughes Medical Institute Janelia Research Campus, Ashburn, Virginia, United States of America
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6
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Vardhan S, Jordan T, Sakiyama-Elbert S. Stem cell engineering approaches for investigating glial cues in central nervous system disorders. Curr Opin Biotechnol 2024; 87:103131. [PMID: 38599012 PMCID: PMC11351366 DOI: 10.1016/j.copbio.2024.103131] [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: 08/16/2023] [Revised: 03/04/2024] [Accepted: 03/26/2024] [Indexed: 04/12/2024]
Abstract
Glial cells are important in maintaining homeostasis for neurons in the central nervous system (CNS). During CNS disease or after injury, glia react to altered microenvironments and often acquire altered functions that contribute to disease pathology. A major focus for research is utilizing stem cell (SC)-derived glia as a potential renewable source for cell replacement to restore function, including neuronal support, and as a model for disease states to identify therapeutic targets. In this review, we focus on SC differentiation protocols for deriving three types of glial cells, astrocytes, oligodendrocytes, and microglia. These SC-derived glia can be used to identify critical cues that contribute to CNS disease progression and aid in investigation of therapeutic targets.
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Affiliation(s)
- Sangamithra Vardhan
- Department of Bioengineering, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Tyler Jordan
- Department of Bioengineering, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Shelly Sakiyama-Elbert
- Department of Bioengineering, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
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7
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Geertsma HM, Fisk ZA, Sauline L, Prigent A, Kurgat K, Callaghan SM, Henderson MX, Rousseaux MWC. A topographical atlas of α-synuclein dosage and cell type-specific expression in adult mouse brain and peripheral organs. NPJ Parkinsons Dis 2024; 10:65. [PMID: 38504090 PMCID: PMC10951202 DOI: 10.1038/s41531-024-00672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease worldwide and presents pathologically with Lewy pathology and dopaminergic neurodegeneration. Lewy pathology contains aggregated α-synuclein (αSyn), a protein encoded by the SNCA gene which is also mutated or duplicated in a subset of familial PD cases. Due to its predominant presynaptic localization, immunostaining for the protein results in a diffuse reactivity pattern, providing little insight into the types of cells expressing αSyn. As a result, insight into αSyn expression-driven cellular vulnerability has been difficult to ascertain. Using a combination of knock-in mice that target αSyn to the nucleus (SncaNLS) and in situ hybridization of Snca in wild-type mice, we systematically mapped the topography and cell types expressing αSyn in the mouse brain, spinal cord, retina, and gut. We find a high degree of correlation between αSyn protein and RNA levels and further identify cell types with low and high αSyn content. We also find high αSyn expression in neurons, particularly those involved in PD, and to a lower extent in non-neuronal cell types, notably those of oligodendrocyte lineage, which are relevant to multiple system atrophy pathogenesis. Surprisingly, we also found that αSyn is relatively absent from select neuron types, e.g., ChAT-positive motor neurons, whereas enteric neurons universally express some degree of αSyn. Together, this integrated atlas provides insight into the cellular topography of αSyn, and provides a quantitative map to test hypotheses about the role of αSyn in network vulnerability, and thus serves investigations into PD pathogenesis and other α-synucleinopathies.
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Affiliation(s)
- Haley M Geertsma
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, K1H8M5, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H8M5, Canada
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Zoe A Fisk
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, K1H8M5, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H8M5, Canada
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Lillian Sauline
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Alice Prigent
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Kevin Kurgat
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Steve M Callaghan
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, K1H8M5, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H8M5, Canada
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Michael X Henderson
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA.
| | - Maxime W C Rousseaux
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, K1H8M5, Canada.
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H8M5, Canada.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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8
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Yang J, Du C, Li Y, Liu R, Jing C, Xie J, Wang J. Contrasting Iron Metabolism in Undifferentiated Versus Differentiated MO3.13 Oligodendrocytes via IL-1β-Induced Iron Regulatory Protein 1. Neurochem Res 2024; 49:466-476. [PMID: 37917337 DOI: 10.1007/s11064-023-04047-y] [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: 08/12/2023] [Revised: 09/28/2023] [Accepted: 10/14/2023] [Indexed: 11/04/2023]
Abstract
Parkinson's disease (PD) is a prevalent neurodegenerative disorder characterized by the loss of dopaminergic neurons and the accumulation of iron in the substantia nigra. While iron accumulation and inflammation are implicated in PD pathogenesis, their impact on oligodendrocytes, the brain's myelin-forming cells, remains elusive. This study investigated the influence of interleukin-1β (IL-1β), an elevated proinflammatory cytokine in PD, on iron-related proteins in MO3.13 oligodendrocytes. We found that IL-1β treatment in undifferentiated MO3.13 oligodendrocytes increased iron regulatory protein 1 and transferrin receptor 1 (TfR1) expression while decreasing ferroportin 1 (FPN1) expression. Consequently, iron uptake was enhanced, and iron release was reduced, leading to intracellular iron accumulation. Conversely, IL-1β treatment in differentiated MO3.13 oligodendrocytes exhibited the opposite effect, with decreased TfR1 expression, increased FPN1 expression, and reduced iron uptake. These findings suggest that IL-1β-induced dysregulation of iron metabolism in oligodendrocytes may contribute to the pathological processes observed in PD. IL-1β can increase the iron content in undifferentiated oligodendrocytes, thus facilitating the differentiation of undifferentiated MO3.13 oligodendrocytes. In differentiated oligodendrocytes, IL-1β may facilitate iron release, providing a potential source of iron for neighboring dopaminergic neurons, thereby initiating a cascade of deleterious events. This study provides valuable insights into the intricate interplay between inflammation, abnormal iron accumulation, and oligodendrocyte dysfunction in PD. Targeting the IL-1β-mediated alterations in iron metabolism may hold therapeutic potential for mitigating neurodegeneration and preserving dopaminergic function in PD.
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Affiliation(s)
- Jiahua Yang
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Chenchen Du
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
- Institute of Senior Care and Art, Guangdong Vocational College of Hotel Management, Dongguan, China
| | - Yinghui Li
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Rong Liu
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Cuiting Jing
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Junxia Xie
- Institute of Brain Science and Disease, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders, Qingdao University, Qingdao, 266071, China
| | - Jun Wang
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China.
- Institute of Brain Science and Disease, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders, Qingdao University, Qingdao, 266071, China.
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9
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Festa LK, Grinspan JB, Jordan-Sciutto KL. White matter injury across neurodegenerative disease. Trends Neurosci 2024; 47:47-57. [PMID: 38052682 PMCID: PMC10842057 DOI: 10.1016/j.tins.2023.11.003] [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: 10/16/2023] [Accepted: 11/11/2023] [Indexed: 12/07/2023]
Abstract
Oligodendrocytes (OLs), the myelin-generating cells of the central nervous system (CNS), are active players in shaping neuronal circuitry and function. It has become increasingly apparent that injury to cells within the OL lineage plays a central role in neurodegeneration. In this review, we focus primarily on three degenerative disorders in which white matter loss is well documented: Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). We discuss clinical data implicating white matter injury as a key feature of these disorders, as well as shared and divergent phenotypes between them. We examine the cellular and molecular mechanisms underlying the alterations to OLs, including chronic neuroinflammation, aggregation of proteins, lipid dysregulation, and organellar stress. Last, we highlight prospects for therapeutic intervention targeting the OL lineage to restore function.
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Affiliation(s)
- Lindsay K Festa
- Department of Oral Medicine, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Judith B Grinspan
- Department of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kelly L Jordan-Sciutto
- Department of Oral Medicine, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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10
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Saramowicz K, Siwecka N, Galita G, Kucharska-Lusina A, Rozpędek-Kamińska W, Majsterek I. Alpha-Synuclein Contribution to Neuronal and Glial Damage in Parkinson's Disease. Int J Mol Sci 2023; 25:360. [PMID: 38203531 PMCID: PMC10778752 DOI: 10.3390/ijms25010360] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disease characterized by the progressive loss of dopaminergic neurons in the substantia nigra and the widespread accumulation of alpha-synuclein (αSyn) protein aggregates. αSyn aggregation disrupts critical cellular processes, including synaptic function, mitochondrial integrity, and proteostasis, which culminate in neuronal cell death. Importantly, αSyn pathology extends beyond neurons-it also encompasses spreading throughout the neuronal environment and internalization by microglia and astrocytes. Once internalized, glia can act as neuroprotective scavengers, which limit the spread of αSyn. However, they can also become reactive, thereby contributing to neuroinflammation and the progression of PD. Recent advances in αSyn research have enabled the molecular diagnosis of PD and accelerated the development of targeted therapies. Nevertheless, despite more than two decades of research, the cellular function, aggregation mechanisms, and induction of cellular damage by αSyn remain incompletely understood. Unraveling the interplay between αSyn, neurons, and glia may provide insights into disease initiation and progression, which may bring us closer to exploring new effective therapeutic strategies. Herein, we provide an overview of recent studies emphasizing the multifaceted nature of αSyn and its impact on both neuron and glial cell damage.
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Affiliation(s)
| | | | | | | | | | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (K.S.); (N.S.); (G.G.); (A.K.-L.); (W.R.-K.)
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11
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Yang K, Wu Z, Long J, Li W, Wang X, Hu N, Zhao X, Sun T. White matter changes in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:150. [PMID: 37907554 PMCID: PMC10618166 DOI: 10.1038/s41531-023-00592-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/17/2023] [Indexed: 11/02/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease after Alzheimer's disease (AD). It is characterized by a progressive loss of dopaminergic neurons in the substantia nigra pars compacta (SNc) and the formation of Lewy bodies (LBs). Although PD is primarily considered a gray matter (GM) disease, alterations in white matter (WM) have gained increasing attention in PD research recently. Here we review evidence collected by magnetic resonance imaging (MRI) techniques which indicate WM abnormalities in PD, and discuss the correlations between WM changes and specific PD symptoms. Then we summarize transcriptome and genome studies showing the changes of oligodendrocyte (OLs)/myelin in PD. We conclude that WM abnormalities caused by the changes of myelin/OLs might be important for PD pathology, which could be potential targets for PD treatment.
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Affiliation(s)
- Kai Yang
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, People's Republic of China.
| | - Zhengqi Wu
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, People's Republic of China
| | - Jie Long
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, People's Republic of China
| | - Wenxin Li
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, People's Republic of China
| | - Xi Wang
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, People's Republic of China
| | - Ning Hu
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, People's Republic of China
| | - Xinyue Zhao
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, People's Republic of China
| | - Taolei Sun
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, People's Republic of China.
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, People's Republic of China.
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12
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Gutierrez BA, González-Coronel JM, Arellano RO, Limon A. Transcriptional and bioinformatic analysis of GABA A receptors expressed in oligodendrocyte progenitor cells from the human brain. Front Mol Neurosci 2023; 16:1279232. [PMID: 37953877 PMCID: PMC10637375 DOI: 10.3389/fnmol.2023.1279232] [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: 08/18/2023] [Accepted: 10/12/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction Oligodendrocyte progenitor cells (OPCs) are vital for neuronal myelination and remyelination in the central nervous system. While the molecular mechanisms involved in OPCs' differentiation and maturation are not completely understood, GABA is known to positively influence these processes through the activation of GABAA receptors (GABAARs). The molecular identity of GABAARs expressed in human OPCs remains unknown, which restricts their specific pharmacological modulation to directly assess their role in oligodendrocytes' maturation and remyelination. Methods In this study, we conducted a transcriptomic analysis to investigate the molecular stoichiometry of GABAARs in OPCs from the human brain. Using eight available transcriptomic datasets from the human brain cortex of control individuals, we analyzed the mRNA expression of all 19 known GABAARs subunit genes in OPCs, with variations observed across different ages. Results Our analysis indicated that the most expressed subunits in OPCs are α1-3, β1-3, γ1-3, and ε. Moreover, we determined that the combination of any α with β2 and γ2 is likely to form heteropentameric GABAARs in OPCs. Importantly, we also found a strong correlation between GABAAR subunits and transcripts for postsynaptic scaffold proteins, suggesting the potential postsynaptic clustering of GABAARs in OPCs. Discussion This study presents the first transcriptional-level identification of GABAAR subunits expressed in human OPCs, providing potential receptor combinations. Understanding the molecular composition of GABAARs in OPCs not only enhances our knowledge of the underlying mechanisms in oligodendrocyte maturation but also opens avenues for targeted pharmacological interventions aimed at modulating these receptors to promote remyelination in neurological disorders.
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Affiliation(s)
- Berenice A. Gutierrez
- Department of Neurology, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States
- Laboratorio de Neurofisiología Celular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Mexico
| | - José Manuel González-Coronel
- Laboratorio de Neurofisiología Celular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Mexico
| | - Rogelio O. Arellano
- Laboratorio de Neurofisiología Celular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Mexico
| | - Agenor Limon
- Department of Neurology, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, United States
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Pomeshchik Y, Velasquez E, Gil J, Klementieva O, Gidlöf R, Sydoff M, Bagnoli S, Nacmias B, Sorbi S, Westergren-Thorsson G, Gouras GK, Rezeli M, Roybon L. Proteomic analysis across patient iPSC-based models and human post-mortem hippocampal tissue reveals early cellular dysfunction and progression of Alzheimer's disease pathogenesis. Acta Neuropathol Commun 2023; 11:150. [PMID: 37715247 PMCID: PMC10504768 DOI: 10.1186/s40478-023-01649-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: 06/03/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023] Open
Abstract
The hippocampus is a primary region affected in Alzheimer's disease (AD). Because AD postmortem brain tissue is not available prior to symptomatic stage, we lack understanding of early cellular pathogenic mechanisms. To address this issue, we examined the cellular origin and progression of AD pathogenesis by comparing patient-based model systems including iPSC-derived brain cells transplanted into the mouse brain hippocampus. Proteomic analysis of the graft enabled the identification of pathways and network dysfunction in AD patient brain cells, associated with increased levels of Aβ-42 and β-sheet structures. Interestingly, the host cells surrounding the AD graft also presented alterations in cellular biological pathways. Furthermore, proteomic analysis across human iPSC-based models and human post-mortem hippocampal tissue projected coherent longitudinal cellular changes indicative of early to end stage AD cellular pathogenesis. Our data showcase patient-based models to study the cell autonomous origin and progression of AD pathogenesis.
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Affiliation(s)
- Yuriy Pomeshchik
- iPSC Laboratory for CNS Disease Modelling, Department of Experimental Medical Science, BMC D10, Lund University, 22184, Lund, Sweden.
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden.
- Lund Stem Cell Center, Lund University, 22184, Lund, Sweden.
| | - Erika Velasquez
- iPSC Laboratory for CNS Disease Modelling, Department of Experimental Medical Science, BMC D10, Lund University, 22184, Lund, Sweden
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden
- Lund Stem Cell Center, Lund University, 22184, Lund, Sweden
| | - Jeovanis Gil
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, BMC D13, Lund University, 22184, Lund, Sweden
| | - Oxana Klementieva
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden
- Medical Micro-Spectroscopy, Department of Experimental Medical Science, BMC B10, Lund University, 22184, Lund, Sweden
| | - Ritha Gidlöf
- Lund University BioImaging Centre, Faculty of Medicine, Lund University, 22142, Lund, Sweden
| | - Marie Sydoff
- Lund University BioImaging Centre, Faculty of Medicine, Lund University, 22142, Lund, Sweden
| | - Silvia Bagnoli
- Laboratorio Di Neurogenetica, Dipartimento Di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino- NEUROFARBA, Università degli Studi di Firenze, 50134, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Benedetta Nacmias
- Laboratorio Di Neurogenetica, Dipartimento Di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino- NEUROFARBA, Università degli Studi di Firenze, 50134, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Sandro Sorbi
- Laboratorio Di Neurogenetica, Dipartimento Di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino- NEUROFARBA, Università degli Studi di Firenze, 50134, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Gunilla Westergren-Thorsson
- Department of Experimental Medical Science, BMC C12, Faculty of Medicine, Lund University, 22142, Lund, Sweden
| | - Gunnar K Gouras
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden
- Experimental Dementia Research Unit, Department of Experimental Medical Science, BMC B11, Lund University, 22184, Lund, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, BMC D13, Lund University, 22184, Lund, Sweden
- Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Lund University, 22184, Lund, Sweden
| | - Laurent Roybon
- iPSC Laboratory for CNS Disease Modelling, Department of Experimental Medical Science, BMC D10, Lund University, 22184, Lund, Sweden.
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden.
- Lund Stem Cell Center, Lund University, 22184, Lund, Sweden.
- Department of Neurodegenerative Science, The MiND Program, Van Andel Institute, Grand Rapids, MI, USA.
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14
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Yang S, Park JH, Lu HC. Axonal energy metabolism, and the effects in aging and neurodegenerative diseases. Mol Neurodegener 2023; 18:49. [PMID: 37475056 PMCID: PMC10357692 DOI: 10.1186/s13024-023-00634-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/08/2023] [Indexed: 07/22/2023] Open
Abstract
Human studies consistently identify bioenergetic maladaptations in brains upon aging and neurodegenerative disorders of aging (NDAs), such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and Amyotrophic lateral sclerosis. Glucose is the major brain fuel and glucose hypometabolism has been observed in brain regions vulnerable to aging and NDAs. Many neurodegenerative susceptible regions are in the topological central hub of the brain connectome, linked by densely interconnected long-range axons. Axons, key components of the connectome, have high metabolic needs to support neurotransmission and other essential activities. Long-range axons are particularly vulnerable to injury, neurotoxin exposure, protein stress, lysosomal dysfunction, etc. Axonopathy is often an early sign of neurodegeneration. Recent studies ascribe axonal maintenance failures to local bioenergetic dysregulation. With this review, we aim to stimulate research in exploring metabolically oriented neuroprotection strategies to enhance or normalize bioenergetics in NDA models. Here we start by summarizing evidence from human patients and animal models to reveal the correlation between glucose hypometabolism and connectomic disintegration upon aging/NDAs. To encourage mechanistic investigations on how axonal bioenergetic dysregulation occurs during aging/NDAs, we first review the current literature on axonal bioenergetics in distinct axonal subdomains: axon initial segments, myelinated axonal segments, and axonal arbors harboring pre-synaptic boutons. In each subdomain, we focus on the organization, activity-dependent regulation of the bioenergetic system, and external glial support. Second, we review the mechanisms regulating axonal nicotinamide adenine dinucleotide (NAD+) homeostasis, an essential molecule for energy metabolism processes, including NAD+ biosynthetic, recycling, and consuming pathways. Third, we highlight the innate metabolic vulnerability of the brain connectome and discuss its perturbation during aging and NDAs. As axonal bioenergetic deficits are developing into NDAs, especially in asymptomatic phase, they are likely exaggerated further by impaired NAD+ homeostasis, the high energetic cost of neural network hyperactivity, and glial pathology. Future research in interrogating the causal relationship between metabolic vulnerability, axonopathy, amyloid/tau pathology, and cognitive decline will provide fundamental knowledge for developing therapeutic interventions.
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Affiliation(s)
- Sen Yang
- The Linda and Jack Gill Center for Biomolecular Sciences, Indiana University, Bloomington, IN, 47405, USA
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, 47405, USA
- Program in Neuroscience, Indiana University, Bloomington, IN, 47405, USA
| | - Jung Hyun Park
- The Linda and Jack Gill Center for Biomolecular Sciences, Indiana University, Bloomington, IN, 47405, USA
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, 47405, USA
- Program in Neuroscience, Indiana University, Bloomington, IN, 47405, USA
| | - Hui-Chen Lu
- The Linda and Jack Gill Center for Biomolecular Sciences, Indiana University, Bloomington, IN, 47405, USA.
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, 47405, USA.
- Program in Neuroscience, Indiana University, Bloomington, IN, 47405, USA.
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15
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Yan YW, Qian ES, Woodard LE, Bejoy J. Neural lineage differentiation of human pluripotent stem cells: Advances in disease modeling. World J Stem Cells 2023; 15:530-547. [PMID: 37424945 PMCID: PMC10324500 DOI: 10.4252/wjsc.v15.i6.530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/14/2023] [Accepted: 04/27/2023] [Indexed: 06/20/2023] Open
Abstract
Brain diseases affect 1 in 6 people worldwide. These diseases range from acute neurological conditions such as stroke to chronic neurodegenerative disorders such as Alzheimer’s disease. Recent advancements in tissue-engineered brain disease models have overcome many of the different shortcomings associated with the various animal models, tissue culture models, and epidemiologic patient data that are commonly used to study brain disease. One innovative method by which to model human neurological disease is via the directed differentiation of human pluripotent stem cells (hPSCs) to neural lineages including neurons, astrocytes, and oligodendrocytes. Three-dimensional models such as brain organoids have also been derived from hPSCs, offering more physiological relevance due to their incorporation of various cell types. As such, brain organoids can better model the pathophysiology of neural diseases observed in patients. In this review, we will emphasize recent developments in hPSC-based tissue culture models of neurological disorders and how they are being used to create neural disease models.
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Affiliation(s)
- Yuan-Wei Yan
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Eddie S Qian
- Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Lauren E Woodard
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, United States
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN 37232, United States
- Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, United States
| | - Julie Bejoy
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, United States
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16
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Lu S, Keleş S. Debiased personalized gene coexpression networks for population-scale scRNA-seq data. Genome Res 2023; 33:932-947. [PMID: 37295843 PMCID: PMC10519377 DOI: 10.1101/gr.277363.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
Population-scale single-cell RNA-seq (scRNA-seq) data sets create unique opportunities for quantifying expression variation across individuals at the gene coexpression network level. Estimation of coexpression networks is well established for bulk RNA-seq; however, single-cell measurements pose novel challenges owing to technical limitations and noise levels of this technology. Gene-gene correlation estimates from scRNA-seq tend to be severely biased toward zero for genes with low and sparse expression. Here, we present Dozer to debias gene-gene correlation estimates from scRNA-seq data sets and accurately quantify network-level variation across individuals. Dozer corrects correlation estimates in the general Poisson measurement model and provides a metric to quantify genes measured with high noise. Computational experiments establish that Dozer estimates are robust to mean expression levels of the genes and the sequencing depths of the data sets. Compared with alternatives, Dozer results in fewer false-positive edges in the coexpression networks, yields more accurate estimates of network centrality measures and modules, and improves the faithfulness of networks estimated from separate batches of the data sets. We showcase unique analyses enabled by Dozer in two population-scale scRNA-seq applications. Coexpression network-based centrality analysis of multiple differentiating human induced pluripotent stem cell (iPSC) lines yields biologically coherent gene groups that are associated with iPSC differentiation efficiency. Application with population-scale scRNA-seq of oligodendrocytes from postmortem human tissues of Alzheimer's disease and controls uniquely reveals coexpression modules of innate immune response with distinct coexpression levels between the diagnoses. Dozer represents an important advance in estimating personalized coexpression networks from scRNA-seq data.
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Affiliation(s)
- Shan Lu
- Department of Statistics, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin, Madison, Wisconsin 53706, USA;
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
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17
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Ogi DA, Jin S. Transcriptome-Powered Pluripotent Stem Cell Differentiation for Regenerative Medicine. Cells 2023; 12:1442. [PMID: 37408278 DOI: 10.3390/cells12101442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 07/07/2023] Open
Abstract
Pluripotent stem cells are endless sources for in vitro engineering human tissues for regenerative medicine. Extensive studies have demonstrated that transcription factors are the key to stem cell lineage commitment and differentiation efficacy. As the transcription factor profile varies depending on the cell type, global transcriptome analysis through RNA sequencing (RNAseq) has been a powerful tool for measuring and characterizing the success of stem cell differentiation. RNAseq has been utilized to comprehend how gene expression changes as cells differentiate and provide a guide to inducing cellular differentiation based on promoting the expression of specific genes. It has also been utilized to determine the specific cell type. This review highlights RNAseq techniques, tools for RNAseq data interpretation, RNAseq data analytic methods and their utilities, and transcriptomics-enabled human stem cell differentiation. In addition, the review outlines the potential benefits of the transcriptomics-aided discovery of intrinsic factors influencing stem cell lineage commitment, transcriptomics applied to disease physiology studies using patients' induced pluripotent stem cell (iPSC)-derived cells for regenerative medicine, and the future outlook on the technology and its implementation.
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Affiliation(s)
- Derek A Ogi
- Department of Biomedical Engineering, Thomas J. Watson College of Engineering and Applied Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - Sha Jin
- Department of Biomedical Engineering, Thomas J. Watson College of Engineering and Applied Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
- Center of Biomanufacturing for Regenerative Medicine, State University of New York at Binghamton, Binghamton, NY 13902, USA
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18
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Lu S, Keleş S. Dozer: Debiased personalized gene co-expression networks for population-scale scRNA-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538290. [PMID: 37163070 PMCID: PMC10168282 DOI: 10.1101/2023.04.25.538290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Population-scale single cell RNA-seq (scRNA-seq) datasets create unique opportunities for quantifying expression variation across individuals at the gene co-expression network level. Estimation of co-expression networks is well-established for bulk RNA-seq; however, single-cell measurements pose novel challenges due to technical limitations and noise levels of this technology. Gene-gene correlation estimates from scRNA-seq tend to be severely biased towards zero for genes with low and sparse expression. Here, we present Dozer to debias gene-gene correlation estimates from scRNA-seq datasets and accurately quantify network level variation across individuals. Dozer corrects correlation estimates in the general Poisson measurement model and provides a metric to quantify genes measured with high noise. Computational experiments establish that Dozer estimates are robust to mean expression levels of the genes and the sequencing depths of the datasets. Compared to alternatives, Dozer results in fewer false positive edges in the co-expression networks, yields more accurate estimates of network centrality measures and modules, and improves the faithfulness of networks estimated from separate batches of the datasets. We showcase unique analyses enabled by Dozer in two population-scale scRNA-seq applications. Co-expression network-based centrality analysis of multiple differentiating human induced pluripotent stem cell (iPSC) lines yields biologically coherent gene groups that are associated with iPSC differentiation efficiency. Application with population-scale scRNA-seq of oligodendrocytes from postmortem human tissues of Alzheimer disease and controls uniquely reveals co-expression modules of innate immune response with markedly different co-expression levels between the diagnoses. Dozer represents an important advance in estimating personalized co-expression networks from scRNA-seq data.
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Affiliation(s)
- Shan Lu
- Department of Statistics, University of Wisconsin, Madison, WI, USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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19
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Shani S, Goldstein O, Gana-Weisz M, Bar-Shira A, Thaler A, Gurevich T, Mirelman A, Giladi N, Alcalay RN, Orr-Urtreger A. Variants in PSMB9 and FGR differentially affect Parkinson's disease risk in GBA and LRRK2 mutation carriers. Parkinsonism Relat Disord 2023; 111:105398. [PMID: 37116292 DOI: 10.1016/j.parkreldis.2023.105398] [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: 01/04/2023] [Revised: 03/16/2023] [Accepted: 04/11/2023] [Indexed: 04/30/2023]
Abstract
INTRODUCTION Recent studies found an association between Parkinson's disease (PD) and alterations in the innate immune system. However, whether the involvement of this system in two of the known genetic forms of PD, GBA-PD and LRRK2-PD, and in patients who do not carry these mutations is different, is yet to be determined. We aimed to test if genetic variations in the innate immune genes are differentially associated with PD in these subgroups. METHODS Innate immune genes were identified and classified into sub-lists according to Reactome pathways. Whole-genome-sequencing (WGS) was performed on 201 unrelated Ashkenazi-Jewish (AJ) PD patients including 104 GBA-PD, 32 LRRK2-PD, and 65 non-carriers-PD (NC-PD). To identify genes with different burden between these subgroups of PD, gene-based Sequence kernel association optimal unified test (SKAT-O) analysis was performed on innate immune pathways. Candidate variants within the significant genes were further genotyped in a cohort of 1200 unrelated, consecutively recruited, AJ-PD patients, and to evaluate their association with PD-risk their allele frequencies were compared to AJ-non-neuro cases in gnomAD database, in a stratified and un-stratified manner. RESULTS SKAT-O analysis showed significantly different burden for PSMB9 (GBA-PD versus NC-PD) and FGR (GBA-PD versus LRRK2-PD). Two candidate variants in PSMB9 showed an association with GBA-PD-risk and NC-PD-risk while one FGR variant showed an association with LRRK2-PD-risk. CONCLUSION Our data supports differential involvement of innate immunity risk alleles in PD and emphasizes the differences between the GBA- and LRRK2-PD subgroups.
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Affiliation(s)
- Shachar Shani
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Orly Goldstein
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
| | - Mali Gana-Weisz
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Anat Bar-Shira
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Avner Thaler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Movement Disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Tanya Gurevich
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Movement Disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Anat Mirelman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Movement Disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Nir Giladi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel; Brain Division Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Roy N Alcalay
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Movement Disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Avi Orr-Urtreger
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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20
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Role of Oligodendrocyte Lineage Cells in Multiple System Atrophy. Cells 2023; 12:cells12050739. [PMID: 36899876 PMCID: PMC10001068 DOI: 10.3390/cells12050739] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Multiple system atrophy (MSA) is a debilitating movement disorder with unknown etiology. Patients present characteristic parkinsonism and/or cerebellar dysfunction in the clinical phase, resulting from progressive deterioration in the nigrostriatal and olivopontocerebellar regions. MSA patients have a prodromal phase subsequent to the insidious onset of neuropathology. Therefore, understanding the early pathological events is important in determining the pathogenesis, which will assist with developing disease-modifying therapy. Although the definite diagnosis of MSA relies on the positive post-mortem finding of oligodendroglial inclusions composed of α-synuclein, only recently has MSA been verified as an oligodendrogliopathy with secondary neuronal degeneration. We review up-to-date knowledge of human oligodendrocyte lineage cells and their association with α-synuclein, and discuss the postulated mechanisms of how oligodendrogliopathy develops, oligodendrocyte progenitor cells as the potential origins of the toxic seeds of α-synuclein, and the possible networks through which oligodendrogliopathy induces neuronal loss. Our insights will shed new light on the research directions for future MSA studies.
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21
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iPSC-Derived Striatal Medium Spiny Neurons from Patients with Multiple System Atrophy Show Hypoexcitability and Elevated α-Synuclein Release. Cells 2023; 12:cells12020223. [PMID: 36672158 PMCID: PMC9856678 DOI: 10.3390/cells12020223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Multiple system atrophy of the parkinsonian type (MSA-P) is a rare, fatal neurodegenerative disease with sporadic onset. It is still unknown if MSA-P is a primary oligodendropathy or caused by neuronal pathophysiology leading to severe, α-synuclein-associated neurodegeneration, mainly in the striatum. In this study, we generated and differentiated induced pluripotent stem cells (iPSCs) from patients with the clinical diagnosis of probable MSA-P (n = 3) and from three matched healthy controls into GABAergic striatal medium spiny neurons (MSNs). We found a significantly elevated release and neuronal distribution for α-synuclein, as well as hypoexcitability in the MSNs derived from the MSA-P patients compared to the healthy controls. These data suggest that the striatal hypoexcitable neurons of MSA-P patients contribute to a pathological α-synuclein burden which is likely to spread to neighboring cells and projection targets, facilitating disease progression.
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22
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Sutter PA, Crocker SJ. Glia as antigen-presenting cells in the central nervous system. Curr Opin Neurobiol 2022; 77:102646. [PMID: 36371828 PMCID: PMC10183975 DOI: 10.1016/j.conb.2022.102646] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/22/2022] [Accepted: 10/06/2022] [Indexed: 11/11/2022]
Abstract
The contribution of the cells within the central nervous system (CNS) toward adaptive immune responses is emerging and incompletely understood. Recent findings indicate important functional interactions between T-cells and glial cells within the CNS that may contribute to disease and neuropathology through antigen presentation. Although glia are not classically considered antigen-presenting cell (APC) types, there is growing evidence indicating that glial antigen presentation plays an important role in several neurological diseases. This review discusses these findings which incriminate microglia, astrocytes, and oligodendrocyte lineage cells as CNS-resident APC types with implications for understanding disease.
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Affiliation(s)
- Pearl A Sutter
- Departments of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Stephen J Crocker
- Departments of Neuroscience, University of Connecticut School of Medicine, Farmington, CT, USA.
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23
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Molina-Gonzalez I, Miron VE, Antel JP. Chronic oligodendrocyte injury in central nervous system pathologies. Commun Biol 2022; 5:1274. [PMID: 36402839 PMCID: PMC9675815 DOI: 10.1038/s42003-022-04248-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022] Open
Abstract
Myelin, the membrane surrounding neuronal axons, is critical for central nervous system (CNS) function. Injury to myelin-forming oligodendrocytes (OL) in chronic neurological diseases (e.g. multiple sclerosis) ranges from sublethal to lethal, leading to OL dysfunction and myelin pathology, and consequent deleterious impacts on axonal health that drive clinical impairments. This is regulated by intrinsic factors such as heterogeneity and age, and extrinsic cellular and molecular interactions. Here, we discuss the responses of OLs to injury, and perspectives for therapeutic targeting. We put forward that targeting mature OL health in neurological disease is a promising therapeutic strategy to support CNS function.
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Affiliation(s)
- Irene Molina-Gonzalez
- grid.4305.20000 0004 1936 7988United Kingdom Dementia Research Institute at The University of Edinburgh, Edinburgh, Scotland UK ,grid.4305.20000 0004 1936 7988Centre for Discovery Brain Sciences, Chancellor’s Building, The University of Edinburgh, Edinburgh, Scotland UK ,grid.4305.20000 0004 1936 7988Medical Research Council Centre for Reproductive Health, The Queen’s Medical Research Institute, The University of Edinburgh, Edinburgh, Scotland UK
| | - Veronique E. Miron
- grid.4305.20000 0004 1936 7988United Kingdom Dementia Research Institute at The University of Edinburgh, Edinburgh, Scotland UK ,grid.4305.20000 0004 1936 7988Centre for Discovery Brain Sciences, Chancellor’s Building, The University of Edinburgh, Edinburgh, Scotland UK ,grid.4305.20000 0004 1936 7988Medical Research Council Centre for Reproductive Health, The Queen’s Medical Research Institute, The University of Edinburgh, Edinburgh, Scotland UK ,grid.415502.7Barlo Multiple Sclerosis Centre and Keenan Research Centre for Biomedical Science, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Immunology, University of Toronto, Toronto, Canada
| | - Jack P. Antel
- grid.14709.3b0000 0004 1936 8649Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, QC Canada
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Kim J, Daadi EW, Oh T, Daadi ES, Daadi MM. Human Induced Pluripotent Stem Cell Phenotyping and Preclinical Modeling of Familial Parkinson's Disease. Genes (Basel) 2022; 13:1937. [PMID: 36360174 PMCID: PMC9689743 DOI: 10.3390/genes13111937] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 12/05/2022] Open
Abstract
Parkinson's disease (PD) is primarily idiopathic and a highly heterogenous neurodegenerative disease with patients experiencing a wide array of motor and non-motor symptoms. A major challenge for understanding susceptibility to PD is to determine the genetic and environmental factors that influence the mechanisms underlying the variations in disease-associated traits. The pathological hallmark of PD is the degeneration of dopaminergic neurons in the substantia nigra pars compacta region of the brain and post-mortem Lewy pathology, which leads to the loss of projecting axons innervating the striatum and to impaired motor and cognitive functions. While the cause of PD is still largely unknown, genome-wide association studies provide evidence that numerous polymorphic variants in various genes contribute to sporadic PD, and 10 to 15% of all cases are linked to some form of hereditary mutations, either autosomal dominant or recessive. Among the most common mutations observed in PD patients are in the genes LRRK2, SNCA, GBA1, PINK1, PRKN, and PARK7/DJ-1. In this review, we cover these PD-related mutations, the use of induced pluripotent stem cells as a disease in a dish model, and genetic animal models to better understand the diversity in the pathogenesis and long-term outcomes seen in PD patients.
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Affiliation(s)
- Jeffrey Kim
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Cell Systems and Anatomy, San Antonio, TX 78229, USA
| | - Etienne W. Daadi
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Thomas Oh
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Elyas S. Daadi
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Marcel M. Daadi
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Cell Systems and Anatomy, San Antonio, TX 78229, USA
- Department of Radiology, Long School of Medicine, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
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