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Research ArticleImmunologyNeuroscience
Open Access | 
10.1172/JCI177793
1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
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Cantoni, C.
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1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
Find articles by Smirnov, R. in: JCI | PubMed | Google Scholar
1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
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1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
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1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
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1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
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1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
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1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
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1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
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1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
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1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
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1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
Find articles by Liu, K. in: JCI | PubMed | Google Scholar
1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
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1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
Find articles by Meyer zu Hörste, G. in: JCI | PubMed | Google Scholar
1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
Find articles by Cross, A. in: JCI | PubMed | Google Scholar
1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
Find articles by Artyomov, M. in: JCI | PubMed | Google Scholar
1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
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1Department of Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona USA.
2Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
3Weill Institute for Neurosciences, UCSF, San Francisco, California, USA.
4Regeneron Pharmaceuticals, Tarrytown, New York, USA.
5Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
6Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.
7Neurology Service, Veterans Affairs St. Louis Health Care System, St. Louis, Missouri, USA.
Address correspondence to: Maxim N. Artyomov or Brian T. Edelson, Department of Pathology and Immunology, Washington University School of Medicine, Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: martyomov@wustl.edu (MNA). Email: bedelson@path.wustl.edu (BTE). Or to: Gregory F. Wu, Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, Missouri 63110, USA. Email: wug@neuro.wustl.edu.
Authorship note: CC and RAS are co–first authors.
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Wu, G.
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Authorship note: CC and RAS are co–first authors.
Published January 2, 2025 - More info
Published in Volume 135, Issue 1 on January 2, 2025
AbstractSingle-cell transcriptomics applied to cerebrospinal fluid (CSF) for elucidating the pathophysiology of neurologic diseases has produced only a preliminary characterization of CSF immune cells. CSF derives from and borders central nervous system (CNS) tissue, allowing for comprehensive accounting of cell types along with their relative abundance and immunologic profiles relevant to CNS diseases. Using integration techniques applied to publicly available datasets in combination with our own studies, we generated a compendium with 139 subjects encompassing 135 CSF and 58 blood samples. Healthy subjects and individuals across a wide range of diseases, such as multiple sclerosis (MS), Alzheimer’s disease, Parkinson’s disease, COVID-19, and autoimmune encephalitis, were included. We found differences in lymphocyte and myeloid subset frequencies across different diseases as well as in their distribution between blood and CSF. We identified what we believe to be a new subset of AREG+ dendritic cells exclusive to the CSF that was more abundant in subjects with MS compared with healthy controls. Finally, transcriptional cell states in CSF microglia-like cells and lymphoid subsets were elucidated. Altogether, we have created a reference compendium for single-cell transcriptional profiling encompassing CSF immune cells useful to the scientific community for future studies on neurologic diseases.
IntroductionHistorically, immune system involvement was considered central to the pathobiology of autoimmune (1), inflammatory, and infectious (2) central nervous system (CNS) diseases. Current diagnostic strategies for various neurologic diseases involve laboratory assessment of blood and cerebrospinal fluid (CSF) components (3, 4). Routine clinical testing of the CSF does not involve deep assessment of its cellular composition, partially because of its usually low concentration of cells and limited availability of material. Several therapeutics alter the CSF cell composition, prompting additional need for comprehensive characterization of CSF immune cells (5, 6). Further, both innate and adaptive arms of the immune system have recently been recognized to play important roles in neurodegenerative diseases (7). An in-depth analysis of the immune cell communities within the CSF affords an opportunity to define disease pathogenesis and treatment responsiveness of different neurologic diseases.
Single-cell transcriptomics is a powerful and rapidly evolving set of technologies that enables the comprehensive characterization of cell heterogeneity at high resolution (8). Single-cell RNA sequencing (scRNA-Seq) facilitates identification of rare and/or low-abundance cell populations that can be masked within bulk cell populations but that may play essential roles in biological processes or disease states. Moreover, scRNA-Seq offers an initial opportunity to address cell ontogeny, compare compartmental microenvironments, and unveil functional traits of various immune cells during health and disease (9).
Several independent studies have explored the composition of human CSF by scRNA-Seq (10–17). As a result, new findings have emerged, including the detection of microglia-like cells found within the CSF but not in blood (17, 18) and identification of distinct lineages such as border-associated macrophages (BAMs) and CXCR6+ resident memory T cells in the CSF (6, 15). However, these studies have used small numbers of samples from individuals with a single neurologic disease, sometimes even without controls, thus returning a highly fragmented view of the CSF micromilieu. Furthermore, single-cell characterization of CSF to date has tended to focus only on specific cell populations (14, 17). Computational advancements including canonical correlation analysis and linear correlation methods only recently have enabled integration of large datasets that reside in public repositories (19, 20), although these compilations have not yet included CSF immune cells. Thus, the opportunity exists to understand the immune cell landscape of the CSF across neurologic diseases.
We therefore have integrated multiple available scRNA-Seq datasets of CSF and peripheral blood mononuclear cell (PBMC) specimens from healthy controls (HC) and subjects with multiple neurologic diseases, including multiple sclerosis (MS), Alzheimer’s disease (AD), Parkinson’s disease, viral encephalitis, HIV-associated neurologic disease, COVID-19, and autoimmune encephalitis, among others. In total, 193 samples were assembled to the dataset comprising 403,973 immune cells (195,431 PBMCs and 208,542 CSF cells). The goal of this study was to identify the diversity of immune cells in neurologic diseases between tissue compartments with the hypothesis that the number and features of various myeloid and lymphoid cell populations within the blood and CSF reflect disease states. Several observations were facilitated by the large number of cells in our compiled dataset. First, based on trajectory inference, we provide evidence that CSF microglia-like cells arise through a BAM lineage from peripheral monocytes. Furthermore, microglia-like cells in the CSF contained FN1+ cells that are uniquely increased in neurodegenerative diseases. Additionally, we identify what we believe to be a new AREG+ type 2 conventional dendritic cell (cDC2) subpopulation in CSF but not blood that is increased in frequency in MS. By redefining and validating the cellular CSF micromilieu at unprecedented depth, we thus identify disease-associated immune populations with future diagnostic potential.
ResultsInitial characterization of PBMC and CSF immune cells in neurologic diseases by scRNA-Seq analysis. We performed a comprehensive analysis of immune cells in the blood and CSF by combining scRNA-Seq datasets from published studies, including some of our own samples (10–18), along with 17 newly acquired samples, including HC and various neurologic diseases (Figure 1A, Table 1, and Supplemental Table 1; supplemental material available online with this article; https://doi.org/10.1172/JCI177793DS1). After integration, a total of 403,973 cells from 58 PBMC (almost exclusively paired with the CSF) and 135 CSF samples were included in the analysis (Figure 1A, Table 1, and Supplemental Table 2). Almost all data were obtained using 10x Genomics with either 5′ or 3′ sequencing (Supplemental Table 3). We first classified 7 main immune cell subsets: myeloid cells, B cells, NK cells, CD4+ and CD8+ T cells, γδ T cells, and plasmacytoid dendritic cells (pDCs). Further analysis of these populations allowed additional discrimination of T helper, microglia-like, and plasmablast cell objects, depicted in a uniform manifold approximation and projection (UMAP) dendrogram in Figure 1B. With more granular cluster dissection, we ultimately identified a total of 51 different cell subpopulations.
Figure 1Cluster hierarchy of overall immune cell type composition from PBMCs and CSF. (A) Schematic representing study design incorporating PBMC and CSF samples (n = 193) from 139 individuals. (B) Dendrogram of UMAP of PBMC and CSF samples colored by cluster and identified by cell type for deeper analysis. Separate objects for subclusters of CD4+ T cells, myeloid cells, and B cells are shown. Total number of cells per object following quality control processing is depicted. See also Supplemental Table 2.
Table 1Cohort characteristics are divided by disease group
The distinction between PBMC and CSF immune cell composition was assessed by separation of these tissues into different objects encompassing 195,431 PBMCs and 208,542 CSF cells (Figure 2, A and B). Annotation of immune cell populations was done based on canonical marker gene expression (Figure 2C). Overall, T lymphoid populations were abundant in the CSF, with the CSF CD4+ T cell cluster being statistically significantly higher compared with PBMCs (Figure 2D). Despite their overall low number, pDCs were also enriched in the CSF compared with PBMCs in a statistically significant manner (Figure 2D). On the contrary, myeloid, B, γδ T, and NK cells were more abundant in PBMCs, consistent with previous reports (12, 18, 21). We next aimed to understand how diseases influenced CSF cells. Because of the vast disease heterogeneity of the sample cohort, we decided to categorize samples into 5 main groups: HC, MS, neurodegenerative diseases (ND), infectious CNS diseases (INF), and other inflammatory diseases of the CNS (OID). Herein, we refer to these disease group names throughout, rather than individual diseases, unless otherwise specified (see Methods). When examining HC alone, the difference in pDC, NK, and B cell abundance between PBMCs and CSF mirrored that seen in the total collection of subjects, although no difference in the CD4+ T cell proportion between PBMCs and CSF was found (Supplemental Figure 1A). The frequency of the PBMC and CSF immune cell populations was unchanged within each disease group with a few notable exceptions. The proportion of CD4+ T cells was dramatically elevated in the CSF of MS subjects (Supplemental Figure 1A). The known numerical predominance of CD4+ T cells in the MS CSF may thus be driven by disease rather than physiology. In sum, these findings indicate a variability in compartmental distribution of immune cells among different neurologic diseases.
Figure 2Differences in composition of major PBMC and CSF cell populations in health and disease. (A and B) UMAP of PBMC (A) and CSF cell (B) atlases color-coded by main cell clusters. (C) Dot plot of marker genes designating each respective cluster. (D) Percentage of total for each major PBMC and CSF cluster. (E) Percentage of total for each CSF cluster across 5 subject groups including 4 disease states. HC, healthy control; MS, multiple sclerosis; ND, neurodegenerative disease; INF, infectious CNS disease; OID, other inflammatory CNS disease. In D and E, whiskers indicate values within 1.5 × interquartile range from either upper or lower hinge. Horizontal bars represent the median value. In D, the test of pairwise comparisons of cell type percentages in PBMCs and CSF was determined by post hoc Dunn’s test with Benjamini-Hochberg adjustment. In E, significance for pairwise comparisons between HC and all other disease groups was determined by post hoc Dunn’s test with Benjamini-Hochberg adjustment. *Adjusted P value (Padj) < 0.05, **Padj < 0.01, ****Padj < 0.0001.
We then analyzed the abundance of different cell populations specifically within the CSF across different disease groups compared with HC (Figure 2E). The proportion of B cells was found to be markedly higher in MS compared with HC, while the reverse was true for myeloid cells. Notably, there was a strong trend for a higher frequency of CD4+ T cells in MS compared with HC that did not reach statistical significance (adjusted P value = 0.056). Also, a statistically significant elevation in the proportion of NK cells within the CSF of ND versus HC was observed (Figure 2E). No other differences in frequencies of other cell populations were apparent, likely because of the small number of samples in the INF and OID disease groups (Table 1). We also examined the proportion of all immune cell subsets within PBMCs from these subjects. We found that, as with CSF, the frequency of B cells was elevated in PBMCs of MS subjects compared with HC as previously described (22, 23) (Supplemental Figure 1B). These findings provide a high-level assessment of the cellular composition and distribution in both CSF and PBMCs across multiple neurologic diseases.
Discrimination of CNS disease state based on PBMC and CSF myeloid cell subpopulations. The myeloid cell object comprised 59,770 cells divided into 36,450 PBMCs and 23,320 CSF cells (Figure 3, A–C). After integration and extensive filtering of the single-cell data, we obtained 13 distinct clusters of myeloid cells. Using established markers (Figure 3D), we identified CD14+ Mono (S100A8, CD14, and VCAN), interferon (Ifn) CD14+ Mono (ISG15, IF44, and IFI44L), CD16+ Mono (FCGR3A, TCF7L2, and CDKN1C), and a small population of neutrophils probably the result of contamination in PBMC preparations (CXCR2, FCGR3B, and G0S2). Seven DC populations were identified in the myeloid object: conventional dendritic cell 1 (cDC1) (CLEC9A, DNASE1L3, and C1orf54); CD32B+ cDC2 (FCGR2B and FCER1A; resembling CD1C_A/DC2 [ref. 24]); CD36+ cDC2 (CD36 and FCN1; akin to CD1C_B/DC3 [ref. 24]); AXL+SIGLEC6+ DCs, which share characteristics with pDCs (AXL, PPP1R14A, and SIGLEC6) (
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