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Elkjaer ML, Hartebrodt A, Oubounyt M, Weber A, Vitved L, Reynolds R, Thomassen M, Rottger R, Baumbach J, Illes Z. Single-Cell Multi-Omics Map of Cell Type-Specific Mechanistic Drivers of Multiple Sclerosis Lesions. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2024; 11:e200213. [PMID: 38564686 PMCID: PMC11073880 DOI: 10.1212/nxi.0000000000200213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/19/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND AND OBJECTIVES In progressive multiple sclerosis (MS), compartmentalized inflammation plays a pivotal role in the complex pathology of tissue damage. The interplay between epigenetic regulation, transcriptional modifications, and location-specific alterations within white matter (WM) lesions at the single-cell level remains underexplored. METHODS We examined intracellular and intercellular pathways in the MS brain WM using a novel dataset obtained by integrated single-cell multi-omics techniques from 3 active lesions, 3 chronic active lesions, 3 remyelinating lesions, and 3 control WM of 6 patients with progressive MS and 3 non-neurologic controls. Single-nucleus RNA-seq and ATAC-seq were combined and additionally enriched with newly conducted spatial transcriptomics from 1 chronic active lesion. Functional gene modules were then validated in our previously published bulk tissue transcriptome data obtained from 73 WM lesions of patients with progressive MS and 25 WM of non-neurologic disease controls. RESULTS Our analysis uncovered an MS-specific oligodendrocyte genetic signature influenced by the KLF/SP gene family. This modulation has potential associations with the autocrine iron uptake signaling observed in transcripts of transferrin and its receptor LRP2. In addition, an inflammatory profile emerged within these oligodendrocytes. We observed unique cellular endophenotypes both at the periphery and within the chronic active lesion. These include a distinct metabolic astrocyte phenotype, the importance of FGF signaling among astrocytes and neurons, and a notable enrichment of mitochondrial genes at the lesion edge populated predominantly by astrocytes. Our study also identified B-cell coexpression networks indicating different functional B-cell subsets with differential location and specific tendencies toward certain lesion types. DISCUSSION The use of single-cell multi-omics has offered a detailed perspective into the cellular dynamics and interactions in MS. These nuanced findings might pave the way for deeper insights into lesion pathogenesis in progressive MS.
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Affiliation(s)
- Maria L Elkjaer
- From the Department of Neurology (M.L.E., A.W., Z.I.), Odense University Hospital; BRIDGE (M.L.E., A.W., M.T., Z.I.), Department of Clinical Research; Department of Molecular Medicine (M.L.E., A.W., L.V., Z.I.), University of Southern Denmark, Odense, Denmark; Biomedical Network Science Lab (A.H.), Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany; Department of Mathematics and Computer Science (A.H., Richard Rottger, J.B.), University of Southern Denmark, Odense, Denmark; Institute for Computational Systems Biology (M.O., J.B.), University of Hamburg, Germany; Department of Brain Sciences (Richard Reynolds), Imperial College, London, United Kingdom; and Clinical Genome Center (M.T.), Research Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Anne Hartebrodt
- From the Department of Neurology (M.L.E., A.W., Z.I.), Odense University Hospital; BRIDGE (M.L.E., A.W., M.T., Z.I.), Department of Clinical Research; Department of Molecular Medicine (M.L.E., A.W., L.V., Z.I.), University of Southern Denmark, Odense, Denmark; Biomedical Network Science Lab (A.H.), Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany; Department of Mathematics and Computer Science (A.H., Richard Rottger, J.B.), University of Southern Denmark, Odense, Denmark; Institute for Computational Systems Biology (M.O., J.B.), University of Hamburg, Germany; Department of Brain Sciences (Richard Reynolds), Imperial College, London, United Kingdom; and Clinical Genome Center (M.T.), Research Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mhaned Oubounyt
- From the Department of Neurology (M.L.E., A.W., Z.I.), Odense University Hospital; BRIDGE (M.L.E., A.W., M.T., Z.I.), Department of Clinical Research; Department of Molecular Medicine (M.L.E., A.W., L.V., Z.I.), University of Southern Denmark, Odense, Denmark; Biomedical Network Science Lab (A.H.), Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany; Department of Mathematics and Computer Science (A.H., Richard Rottger, J.B.), University of Southern Denmark, Odense, Denmark; Institute for Computational Systems Biology (M.O., J.B.), University of Hamburg, Germany; Department of Brain Sciences (Richard Reynolds), Imperial College, London, United Kingdom; and Clinical Genome Center (M.T.), Research Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Anna Weber
- From the Department of Neurology (M.L.E., A.W., Z.I.), Odense University Hospital; BRIDGE (M.L.E., A.W., M.T., Z.I.), Department of Clinical Research; Department of Molecular Medicine (M.L.E., A.W., L.V., Z.I.), University of Southern Denmark, Odense, Denmark; Biomedical Network Science Lab (A.H.), Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany; Department of Mathematics and Computer Science (A.H., Richard Rottger, J.B.), University of Southern Denmark, Odense, Denmark; Institute for Computational Systems Biology (M.O., J.B.), University of Hamburg, Germany; Department of Brain Sciences (Richard Reynolds), Imperial College, London, United Kingdom; and Clinical Genome Center (M.T.), Research Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lars Vitved
- From the Department of Neurology (M.L.E., A.W., Z.I.), Odense University Hospital; BRIDGE (M.L.E., A.W., M.T., Z.I.), Department of Clinical Research; Department of Molecular Medicine (M.L.E., A.W., L.V., Z.I.), University of Southern Denmark, Odense, Denmark; Biomedical Network Science Lab (A.H.), Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany; Department of Mathematics and Computer Science (A.H., Richard Rottger, J.B.), University of Southern Denmark, Odense, Denmark; Institute for Computational Systems Biology (M.O., J.B.), University of Hamburg, Germany; Department of Brain Sciences (Richard Reynolds), Imperial College, London, United Kingdom; and Clinical Genome Center (M.T.), Research Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Richard Reynolds
- From the Department of Neurology (M.L.E., A.W., Z.I.), Odense University Hospital; BRIDGE (M.L.E., A.W., M.T., Z.I.), Department of Clinical Research; Department of Molecular Medicine (M.L.E., A.W., L.V., Z.I.), University of Southern Denmark, Odense, Denmark; Biomedical Network Science Lab (A.H.), Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany; Department of Mathematics and Computer Science (A.H., Richard Rottger, J.B.), University of Southern Denmark, Odense, Denmark; Institute for Computational Systems Biology (M.O., J.B.), University of Hamburg, Germany; Department of Brain Sciences (Richard Reynolds), Imperial College, London, United Kingdom; and Clinical Genome Center (M.T.), Research Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mads Thomassen
- From the Department of Neurology (M.L.E., A.W., Z.I.), Odense University Hospital; BRIDGE (M.L.E., A.W., M.T., Z.I.), Department of Clinical Research; Department of Molecular Medicine (M.L.E., A.W., L.V., Z.I.), University of Southern Denmark, Odense, Denmark; Biomedical Network Science Lab (A.H.), Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany; Department of Mathematics and Computer Science (A.H., Richard Rottger, J.B.), University of Southern Denmark, Odense, Denmark; Institute for Computational Systems Biology (M.O., J.B.), University of Hamburg, Germany; Department of Brain Sciences (Richard Reynolds), Imperial College, London, United Kingdom; and Clinical Genome Center (M.T.), Research Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Richard Rottger
- From the Department of Neurology (M.L.E., A.W., Z.I.), Odense University Hospital; BRIDGE (M.L.E., A.W., M.T., Z.I.), Department of Clinical Research; Department of Molecular Medicine (M.L.E., A.W., L.V., Z.I.), University of Southern Denmark, Odense, Denmark; Biomedical Network Science Lab (A.H.), Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany; Department of Mathematics and Computer Science (A.H., Richard Rottger, J.B.), University of Southern Denmark, Odense, Denmark; Institute for Computational Systems Biology (M.O., J.B.), University of Hamburg, Germany; Department of Brain Sciences (Richard Reynolds), Imperial College, London, United Kingdom; and Clinical Genome Center (M.T.), Research Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jan Baumbach
- From the Department of Neurology (M.L.E., A.W., Z.I.), Odense University Hospital; BRIDGE (M.L.E., A.W., M.T., Z.I.), Department of Clinical Research; Department of Molecular Medicine (M.L.E., A.W., L.V., Z.I.), University of Southern Denmark, Odense, Denmark; Biomedical Network Science Lab (A.H.), Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany; Department of Mathematics and Computer Science (A.H., Richard Rottger, J.B.), University of Southern Denmark, Odense, Denmark; Institute for Computational Systems Biology (M.O., J.B.), University of Hamburg, Germany; Department of Brain Sciences (Richard Reynolds), Imperial College, London, United Kingdom; and Clinical Genome Center (M.T.), Research Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Zsolt Illes
- From the Department of Neurology (M.L.E., A.W., Z.I.), Odense University Hospital; BRIDGE (M.L.E., A.W., M.T., Z.I.), Department of Clinical Research; Department of Molecular Medicine (M.L.E., A.W., L.V., Z.I.), University of Southern Denmark, Odense, Denmark; Biomedical Network Science Lab (A.H.), Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany; Department of Mathematics and Computer Science (A.H., Richard Rottger, J.B.), University of Southern Denmark, Odense, Denmark; Institute for Computational Systems Biology (M.O., J.B.), University of Hamburg, Germany; Department of Brain Sciences (Richard Reynolds), Imperial College, London, United Kingdom; and Clinical Genome Center (M.T.), Research Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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Oikawa K, Ver Hoeve JN, Teixeira LBC, Snyder KC, Kiland JA, Ellinwood NM, McLellan GJ. Sub-region-Specific Optic Nerve Head Glial Activation in Glaucoma. Mol Neurobiol 2020; 57:2620-2638. [PMID: 32266645 DOI: 10.1007/s12035-020-01910-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/23/2020] [Indexed: 12/22/2022]
Abstract
Glaucoma, a multifactorial neurodegenerative disease characterized by progressive loss of retinal ganglion cells and their axons in the optic nerve, is a leading cause of irreversible vision loss. Intraocular pressure (IOP) is a risk factor for axonal damage, which initially occurs at the optic nerve head (ONH). Complex cellular and molecular mechanisms involved in the pathogenesis of glaucomatous optic neuropathy remain unclear. Here we define early molecular events in the ONH in an inherited large animal glaucoma model in which ONH structure resembles that of humans. Gene expression profiling of ONH tissues from rigorously phenotyped feline subjects with early-stage glaucoma and precisely age-matched controls was performed by RNA-sequencing (RNA-seq) analysis and complementary bioinformatic approaches applied to identify molecular processes and pathways of interest. Immunolabeling supported RNA-seq findings while providing cell-, region-, and disease stage-specific context in the ONH in situ. Transcriptomic evidence for cell proliferation and immune/inflammatory responses is identifiable in early glaucoma, soon after IOP elevation and prior to morphologically detectable axon loss, in this large animal model. In particular, proliferation of microglia and oligodendrocyte precursor cells is a prominent feature of early-stage, but not chronic, glaucoma. ONH microgliosis is a consistent hallmark in both early and chronic stages of glaucoma. Molecular pathways and cell type-specific responses strongly implicate toll-like receptor and NF-κB signaling in early glaucoma pathophysiology. The current study provides critical insights into molecular pathways, highly dependent on cell type and sub-region in the ONH even prior to irreversible axon degeneration in glaucoma.
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Affiliation(s)
- Kazuya Oikawa
- Department of Surgical Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI, 53706, USA
- McPherson Eye Research Institute, Madison, WI, USA
| | - James N Ver Hoeve
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI, 53706, USA
- McPherson Eye Research Institute, Madison, WI, USA
| | - Leandro B C Teixeira
- McPherson Eye Research Institute, Madison, WI, USA
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Kevin C Snyder
- Department of Surgical Sciences, University of Wisconsin-Madison, Madison, WI, USA
- McPherson Eye Research Institute, Madison, WI, USA
| | - Julie A Kiland
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI, 53706, USA
| | | | - Gillian J McLellan
- Department of Surgical Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI, 53706, USA.
- McPherson Eye Research Institute, Madison, WI, USA.
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