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Kodali MC, Antone J, Alsop E, Jayakumar R, Parikh K, Chiot A, Sanchez-Molina P, Ajami B, Arnold SE, Jensen K, Das S, Weinberg MS. Cryopreservation of cerebrospinal fluid cells preserves the transcriptional landscape for single-cell analysis. J Neuroinflammation 2024; 21:71. [PMID: 38521932 PMCID: PMC10960996 DOI: 10.1186/s12974-024-03047-1] [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: 10/04/2023] [Accepted: 02/14/2024] [Indexed: 03/25/2024] Open
Abstract
Cerebrospinal fluid (CSF) matrix biomarkers have become increasingly valuable surrogate markers of neuropsychiatric diseases in research and clinical practice. In contrast, CSF cells have been rarely investigated due to their relative scarcity and fragility, and lack of common collection and cryopreservation protocols, with limited exceptions for neurooncology and primary immune-based diseases like multiple sclerosis. the advent of a microfluidics-based multi-omics approach to studying individual cells has allowed for the study of cellular phenotyping, intracellular dynamics, and intercellular relationships that provide multidimensionality unable to be obtained through acellular fluid-phase analyses. challenges to cell-based research include site-to-site differences in handling, storage, and thawing methods, which can lead to inaccuracy and inter-assay variability. In the present study, we performed single-cell RNA sequencing (10x Genomics) on fresh or previously cryopreserved human CSF samples from three alternative cryopreservation methods: Fetal Bovine Serum with Dimethyl sulfoxide (FBS/DMSO), FBS/DMSO after a DNase step (a step often included in epigenetic studies), and cryopreservation using commercially available Recovery© media. In comparing relative differences between fresh and cryopreserved samples, we found little effect of the cryopreservation method on being able to resolve donor-linked cell type proportions, markers of cellular stress, and overall gene expression at the single-cell level, whereas donor-specific differences were readily discernable. We further demonstrate the compatibility of fresh and cryopreserved CSF immune cell sequencing using biologically relevant sexually dimorphic gene expression differences by donor. Our findings support the utility and interchangeability of FBS/DMSO and Recovery cryopreservation with fresh sample analysis, providing a methodological grounding that will enable researchers to further expand our understanding of the CSF immune cell contributions to neurological and psychiatric disease.
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Affiliation(s)
- Mahesh Chandra Kodali
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Jerry Antone
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Eric Alsop
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Khushi Parikh
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Aude Chiot
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
- Department of Behavioral and Systems Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Paula Sanchez-Molina
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
- Department of Behavioral and Systems Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Bahareh Ajami
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
- Department of Behavioral and Systems Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Steven E Arnold
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kendall Jensen
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Sudeshna Das
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Marc S Weinberg
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
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2
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Dyer AH, Dolphin H, O'Connor A, Morrison L, Sedgwick G, McFeely A, Killeen E, Gallagher C, Davey N, Connolly E, Lyons S, Young C, Gaffney C, Ennis R, McHale C, Joseph J, Knight G, Kelly E, O'Farrelly C, Bourke NM, Fallon A, O'Dowd S, Kennelly SP. Protocol for the Tallaght University Hospital Institute for Memory and Cognition-Biobank for Research in Ageing and Neurodegeneration. BMJ Open 2023; 13:e077772. [PMID: 38070888 PMCID: PMC10729202 DOI: 10.1136/bmjopen-2023-077772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
INTRODUCTION Alzheimer's disease and other dementias affect >50 million individuals globally and are characterised by broad clinical and biological heterogeneity. Cohort and biobank studies have played a critical role in advancing the understanding of disease pathophysiology and in identifying novel diagnostic and treatment approaches. However, further discovery and validation cohorts are required to clarify the real-world utility of new biomarkers, facilitate research into the development of novel therapies and advance our understanding of the clinical heterogeneity and pathobiology of neurodegenerative diseases. METHODS AND ANALYSIS The Tallaght University Hospital Institute for Memory and Cognition Biobank for Research in Ageing and Neurodegeneration (TIMC-BRAiN) will recruit 1000 individuals over 5 years. Participants, who are undergoing diagnostic workup in the TIMC Memory Assessment and Support Service (TIMC-MASS), will opt to donate clinical data and biological samples to a biobank. All participants will complete a detailed clinical, neuropsychological and dementia severity assessment (including Addenbrooke's Cognitive Assessment, Repeatable Battery for Assessment of Neuropsychological Status, Clinical Dementia Rating Scale). Participants undergoing venepuncture/lumbar puncture as part of the clinical workup will be offered the opportunity to donate additional blood (serum/plasma/whole blood) and cerebrospinal fluid samples for longitudinal storage in the TIMC-BRAiN biobank. Participants are followed at 18-month intervals for repeat clinical and cognitive assessments. Anonymised clinical data and biological samples will be stored securely in a central repository and used to facilitate future studies concerned with advancing the diagnosis and treatment of neurodegenerative diseases. ETHICS AND DISSEMINATION Ethical approval has been granted by the St. James's Hospital/Tallaght University Hospital Joint Research Ethics Committee (Project ID: 2159), which operates in compliance with the European Communities (Clinical Trials on Medicinal Products for Human Use) Regulations 2004 and ICH Good Clinical Practice Guidelines. Findings using TIMC-BRAiN will be published in a timely and open-access fashion.
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Affiliation(s)
- Adam H Dyer
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
- Discipline of Medical Gerontology, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Helena Dolphin
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
- Discipline of Medical Gerontology, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Laura Morrison
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
- Discipline of Medical Gerontology, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Gavin Sedgwick
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
| | - Aoife McFeely
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
- Discipline of Medical Gerontology, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Emily Killeen
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
| | - Conal Gallagher
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
| | - Naomi Davey
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
| | - Eimear Connolly
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
| | - Shane Lyons
- Department of Neurology, Tallaght University Hospital, Dublin, Ireland
| | - Conor Young
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
| | - Christine Gaffney
- Department of Neurology, Tallaght University Hospital, Dublin, Ireland
| | - Ruth Ennis
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
| | - Cathy McHale
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
| | - Jasmine Joseph
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
| | - Graham Knight
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
| | - Emmet Kelly
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
| | | | - Nollaig M Bourke
- Discipline of Medical Gerontology, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Aoife Fallon
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
- Discipline of Medical Gerontology, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Sean O'Dowd
- Department of Neurology, Tallaght University Hospital, Dublin, Ireland
- Academic Unit of Neurology, Trinity College Dublin, Dublin, Ireland
| | - Sean P Kennelly
- Institute of Memory and Cognition, Tallaght University Hospital, Dublin, Ireland
- Discipline of Medical Gerontology, School of Medicine, Trinity College Dublin, Dublin, Ireland
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3
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Touil H, Roostaei T, Calini D, Diaconu C, Epstein S, Raposo C, Onomichi K, Thakur KT, Craveiro L, Callegari I, Bryois J, Riley CS, Menon V, Derfuss T, De Jager PL, Malhotra D. A structured evaluation of cryopreservation in generating single-cell transcriptomes from cerebrospinal fluid. CELL REPORTS METHODS 2023; 3:100533. [PMID: 37533636 PMCID: PMC10391561 DOI: 10.1016/j.crmeth.2023.100533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/28/2023] [Accepted: 06/21/2023] [Indexed: 08/04/2023]
Abstract
Single-cell transcriptomics allows characterization of cerebrospinal fluid (CSF) cells at an unprecedented level. Here, we report a robust cryopreservation protocol adapted for the characterization of fragile CSF cells by single-cell RNA sequencing (RNA-seq) in moderate- to large-scale studies. Fresh CSF was collected from twenty-one participants at two independent sites. Each CSF sample was split into two fractions: one was processed fresh, while the second was cryopreserved for months and profiled after thawing. B and T cell receptor sequencing was also performed. Our comparison of fresh and cryopreserved data from the same individuals demonstrates highly efficient recovery of all known CSF cell types. We find no significant difference in cell type proportions and cellular transcriptomes between fresh and cryopreserved cells. Results were comparable at both sites and with different single-cell sequencing chemistries. Cryopreservation did not affect recovery of T and B cell clonotype diversity. Our CSF cell cryopreservation protocol provides an important alternative to fresh processing of fragile CSF cells.
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Affiliation(s)
- Hanane Touil
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tina Roostaei
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Daniela Calini
- Neuroscience and Rare Diseases (NRD), F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, 4070 Basel, Switzerland
| | - Claudiu Diaconu
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samantha Epstein
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Catarina Raposo
- gRED OMNI-Biomarker Development, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, Basel, Switzerland
| | - Kaho Onomichi
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kiran T. Thakur
- Program in Neuroinfectious Diseases, Division of Critical Care and Hospitalist Neurology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Licinio Craveiro
- Product Development Medical Affairs (PDMA) Neuroscience, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, 4070 Basel, Switzerland
| | - Ilaria Callegari
- University Hospital Basel, Department of Neurology and Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Julien Bryois
- Neuroscience and Rare Diseases (NRD), F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, 4070 Basel, Switzerland
| | - Claire S. Riley
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vilas Menon
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tobias Derfuss
- University Hospital Basel, Department of Neurology and Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dheeraj Malhotra
- Neuroscience and Rare Diseases (NRD), F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, 4070 Basel, Switzerland
- MS Research Unit, Biogen, Cambridge, MA 02142, USA
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4
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Wang H, Wu H, Li KD, Wang YY, Huang RG, Du YJ, Jin X, Zhang QR, Li XB, Li BZ. Intestinal fungi and systemic autoimmune diseases. Autoimmun Rev 2023; 22:103234. [PMID: 36423833 DOI: 10.1016/j.autrev.2022.103234] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]
Abstract
Nearly 20 years of studies have shown that fungi and the human immune system (non-specific immunity and specific immunity) and bacterial--fungal interactions maintain a balance that can't lead to diseases. Fungi--microorganism that lives in human intestine--may play an important role in human health and disease. Population studies and animal models in some diseases have found the changes in the diversity and composition of fungi. The dysregulation of the fungi can disrupt the normal "running" of the immune system and bacteria, which triggers the development of inflammatory diseases. The latest studies of fungi in inflammatory bowel disease, systemic lupus erythematosus, ankylosing spondylitis and type 1 diabetes mellitus were summarized. This review considers how the healthy host protect against the potential harm of intestinal fungi through the immune system and how fungal dysregulation alters host immunity.
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Affiliation(s)
- Hua Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Hong Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Kai-Di Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yi-Yu Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Rong-Gui Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yu-Jie Du
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Xue Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Qian-Ru Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China; Department of Cardiovascular Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Xian-Bao Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Bao-Zhu Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China.
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5
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Piehl N, van Olst L, Ramakrishnan A, Teregulova V, Simonton B, Zhang Z, Tapp E, Channappa D, Oh H, Losada PM, Rutledge J, Trelle AN, Mormino EC, Elahi F, Galasko DR, Henderson VW, Wagner AD, Wyss-Coray T, Gate D. Cerebrospinal fluid immune dysregulation during healthy brain aging and cognitive impairment. Cell 2022; 185:5028-5039.e13. [PMID: 36516855 PMCID: PMC9815831 DOI: 10.1016/j.cell.2022.11.019] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/27/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022]
Abstract
Cerebrospinal fluid (CSF) contains a tightly regulated immune system. However, knowledge is lacking about how CSF immunity is altered with aging or neurodegenerative disease. Here, we performed single-cell RNA sequencing on CSF from 45 cognitively normal subjects ranging from 54 to 82 years old. We uncovered an upregulation of lipid transport genes in monocytes with age. We then compared this cohort with 14 cognitively impaired subjects. In cognitively impaired subjects, downregulation of lipid transport genes in monocytes occurred concomitantly with altered cytokine signaling to CD8 T cells. Clonal CD8 T effector memory cells upregulated C-X-C motif chemokine receptor 6 (CXCR6) in cognitively impaired subjects. The CXCR6 ligand, C-X-C motif chemokine ligand 16 (CXCL16), was elevated in the CSF of cognitively impaired subjects, suggesting CXCL16-CXCR6 signaling as a mechanism for antigen-specific T cell entry into the brain. Cumulatively, these results reveal cerebrospinal fluid immune dysregulation during healthy brain aging and cognitive impairment.
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Affiliation(s)
- Natalie Piehl
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lynn van Olst
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Abhirami Ramakrishnan
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Victoria Teregulova
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Brooke Simonton
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ziyang Zhang
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Emma Tapp
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Divya Channappa
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Hamilton Oh
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Graduate Program in Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Patricia M Losada
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Jarod Rutledge
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Elizabeth C Mormino
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA; Department of Psychology, Stanford University, Stanford, CA, USA
| | - Fanny Elahi
- Departments of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, La Jolla, CA, USA
| | - Douglas R Galasko
- Department of Neurosciences, University of California at San Diego, La Jolla, CA, USA
| | - Victor W Henderson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Anthony D Wagner
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA; Department of Psychology, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; The Phil and Penny Initiative for Brain Resilience, Stanford University, Stanford, CA, USA; Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - David Gate
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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6
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Mexhitaj I, Lim N, Fernandez-Velasco JI, Zrzavy T, Harris KM, Muraro PA, Villar LM, Bar-Or A, Cooney LA. Stabilization of leukocytes from cerebrospinal fluid for central immunophenotypic evaluation in multicenter clinical trials. J Immunol Methods 2022; 510:113344. [PMID: 36041516 DOI: 10.1016/j.jim.2022.113344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 12/31/2022]
Abstract
Analysis of cerebrospinal fluid (CSF) represents a valuable window into the pathogenesis of neuroinflammatory diseases, such as multiple sclerosis (MS). However, analysis of the cellular fraction of CSF is often neglected because CSF cells die rapidly ex vivo. Immunophenotyping of CSF cells in multicenter clinical trials requires sample preservation and shipping to a centralized lab. Yet, there is no consensus on the best method to preserve intact CSF cells and no detailed evaluation of subset-specific cell loss. We used flow cytometry to compare major leukocyte populations in fresh CSF (processed within 2 h) to cells fixed for 48 h with TransFix-EDTA® or cryopreserved and thawed after 96 h. We observed a statistically significant loss of total mononuclear cells, total T cells, CD3+ CD8- T cells, and CD3+ CD8+ T cells after cryopreservation compared to fresh or fixed (p < 0.001), with no significant difference between fresh and fixed. Thus, our results demonstrate that TransFix-EDTA® was superior to cryopreservation for preserving intact CSF T cells. Surprisingly, neither cryopreservation nor fixation had a significant effect on recovery of low frequency cell subsets in CSF, including B cells, NK cells, NKT-like cells, CD14+ monocytes, or CD123+ DCs, versus fresh CSF. To determine the effect of prolonged fixation on cell recovery, we analyzed major CSF cell subsets by flow cytometry after 24, 48, or 72 h of fixation with TransFix-EDTA®. We observed a consistent and progressive loss in the absolute counts of all subsets over time, although this effect was not statistically significant. We conclude that for immunophenotyping of major CSF cell subsets by flow cytometry, fixation with TransFix-EDTA®, shipment to a central lab, and analysis within 48 h is a feasible method to ensure stability of both absolute cell number and relative frequency. This method is a valuable alternative to fresh CSF analysis and can be implemented in multicenter clinical trials.
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Affiliation(s)
- Ina Mexhitaj
- Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Noha Lim
- Immune Tolerance Network, Bethesda, MD, USA
| | | | - Tobias Zrzavy
- Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Paolo A Muraro
- Department of Brain Sciences, Imperial College London, London, UK
| | - Luisa M Villar
- Department of Immunology, Hospital Ramón y Cajal, Madrid, Spain
| | - Amit Bar-Or
- Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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7
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Heming M, Börsch AL, Wiendl H, Meyer Zu Hörste G. High-dimensional investigation of the cerebrospinal fluid to explore and monitor CNS immune responses. Genome Med 2022; 14:94. [PMID: 35978442 PMCID: PMC9385102 DOI: 10.1186/s13073-022-01097-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/28/2022] [Indexed: 01/15/2023] Open
Abstract
The cerebrospinal fluid (CSF) features a unique immune cell composition and is in constant contact with the brain borders, thus permitting insights into the brain to diagnose and monitor diseases. Recently, the meninges, which are filled with CSF, were identified as a neuroimmunological interface, highlighting the potential of exploring central nervous system (CNS) immunity by studying CNS border compartments. Here, we summarize how single-cell transcriptomics of such border compartments advance our understanding of neurological diseases, the challenges that remain, and what opportunities novel multi-omic methods offer. Single-cell transcriptomics studies have detected cytotoxic CD4+ T cells and clonally expanded T and B cells in the CSF in the autoimmune disease multiple sclerosis; clonally expanded pathogenic CD8+ T cells were found in the CSF and in the brain adjacent to β-amyloid plaques of dementia patients; in patients with brain metastases, CD8+ T cell clonotypes were shared between the brain parenchyma and the CSF and persisted after therapy. We also outline how novel multi-omic approaches permit the simultaneous measurements of gene expression, chromatin accessibility, and protein in the same cells, which remain to be explored in the CSF. This calls for multicenter initiatives to create single-cell atlases, posing challenges in integrating patients and modalities across centers. While high-dimensional analyses of CSF cells are challenging, they hold potential for personalized medicine by better resolving heterogeneous diseases and stratifying patients.
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Affiliation(s)
- Michael Heming
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Anna-Lena Börsch
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Heinz Wiendl
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Gerd Meyer Zu Hörste
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
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8
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Hörner M, Groh J, Klein D, Ilg W, Schöls L, Santos SD, Bergmann A, Klebe S, Cauhape M, Branchu J, El Hachimi KH, Stevanin G, Darios F, Martini R. CNS-associated T-lymphocytes in a mouse model of Hereditary Spastic Paraplegia type 11 (SPG11) are therapeutic targets for established immunomodulators. Exp Neurol 2022; 355:114119. [DOI: 10.1016/j.expneurol.2022.114119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 11/04/2022]
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9
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Otto F, Harrer C, Pilz G, Wipfler P, Harrer A. Role and Relevance of Cerebrospinal Fluid Cells in Diagnostics and Research: State-of-the-Art and Underutilized Opportunities. Diagnostics (Basel) 2021; 12:diagnostics12010079. [PMID: 35054246 PMCID: PMC8774636 DOI: 10.3390/diagnostics12010079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/07/2021] [Accepted: 12/28/2021] [Indexed: 01/15/2023] Open
Abstract
Cerebrospinal fluid (CSF) has recently experienced a revival in diagnostics and research. However, little progress has been made regarding CSF cell analysis. For almost a century, CSF cell count and cytomorphological examination have been central diagnostic parameters, with CSF pleocytosis as a hallmark finding of neuroinflammation and cytology offering valuable clues regarding infectious, autoimmune, and malignant aetiologies. A great deal of information, however, remains unattended as modern immune phenotyping technologies have not yet been broadly incorporated into routine CSF analysis. This is a serious deficit considering the central role of CSF cells as effectors in central nervous system (CNS) immune defence and autoimmune CNS processes, and the diagnostic challenges posed by clinically overlapping infectious and immune-mediated CNS diseases. Here, we summarize historical, specimen-intrinsic, methodological, and technical issues determining the state-of-the-art diagnostics of CSF cells and outline future perspectives for this underutilized window into meningeal and CNS immunity.
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Affiliation(s)
- Ferdinand Otto
- Department of Neurology, Paracelsus Medical University, Christian-Doppler-Klinik, 5020 Salzburg, Austria; (F.O.); (C.H.); (G.P.); (P.W.)
| | - Christine Harrer
- Department of Neurology, Paracelsus Medical University, Christian-Doppler-Klinik, 5020 Salzburg, Austria; (F.O.); (C.H.); (G.P.); (P.W.)
| | - Georg Pilz
- Department of Neurology, Paracelsus Medical University, Christian-Doppler-Klinik, 5020 Salzburg, Austria; (F.O.); (C.H.); (G.P.); (P.W.)
| | - Peter Wipfler
- Department of Neurology, Paracelsus Medical University, Christian-Doppler-Klinik, 5020 Salzburg, Austria; (F.O.); (C.H.); (G.P.); (P.W.)
| | - Andrea Harrer
- Department of Neurology, Paracelsus Medical University, Christian-Doppler-Klinik, 5020 Salzburg, Austria; (F.O.); (C.H.); (G.P.); (P.W.)
- Department of Dermatology and Allergology, Paracelsus Medical University, Landeskrankenhaus, 5020 Salzburg, Austria
- Correspondence:
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Emerging Single-cell Approaches to Understand HIV in the Central Nervous System. Curr HIV/AIDS Rep 2021; 19:113-120. [PMID: 34822063 PMCID: PMC8613726 DOI: 10.1007/s11904-021-00586-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2021] [Indexed: 11/23/2022]
Abstract
Purpose of Review This review highlights emerging single-cell sequencing methods relevant to translational studies of HIV in the central nervous system (CNS), summarizes limited single-cell studies of HIV in the CNS, and discusses opportunities for future HIV translational CNS studies. Recent Findings Innovative methods utilizing single-cell technologies have advanced the study of genomes, proteomes, transcriptomes, and epigenomes at an enhanced resolution and depth. Single-cell analyses of central nervous system tissue, including autopsy brain and CSF cells, may shed light on CNS perturbations in people living with HIV. New strategies can distinguish distinct molecular identifies of rare infected cells at single-cell level, suggesting an opportunity to uncloak the molecular identity of hidden HIV in the CNS reservoir. Summary Adoption of multimodal “omics” analyses to translational HIV studies and tissue compartments beyond blood will be critical to advancing our understanding of viral establishment, persistence, and eradication.
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11
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Gate D, Tapp E, Leventhal O, Shahid M, Nonninger TJ, Yang AC, Strempfl K, Unger MS, Fehlmann T, Oh H, Channappa D, Henderson VW, Keller A, Aigner L, Galasko DR, Davis MM, Poston KL, Wyss-Coray T. CD4 + T cells contribute to neurodegeneration in Lewy body dementia. Science 2021; 374:868-874. [PMID: 34648304 PMCID: PMC9122025 DOI: 10.1126/science.abf7266] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Recent studies indicate that the adaptive immune system plays a role in Lewy body dementia (LBD). However, the mechanism regulating T cell brain homing in LBD is unknown. Here, we observed T cells adjacent to Lewy bodies and dopaminergic neurons in post-mortem LBD brains. Single-cell RNA sequencing of cerebrospinal fluid (CSF) identified upregulated expression of C-X-C Motif Chemokine Receptor 4 (CXCR4) in CD4+ T cells in LBD. CSF protein levels of the CXCR4 ligand, C-X-C Motif Chemokine Ligand 12 (CXCL12) were associated with neuroaxonal damage in LBD. Furthermore, we observed clonal expansion and upregulated Interleukin 17A expression by CD4+ T cells stimulated with a phosphorylated α-synuclein epitope. Thus, CXCR4-CXCL12 signaling may represent a mechanistic target for inhibiting pathological interleukin-17-producing T cell trafficking in LBD. The immune system is implicated in the neurodegenerative process of Lewy body dementia.
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Affiliation(s)
- David Gate
- Department of Neurology, Northwestern University, Chicago, IL, USA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Emma Tapp
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Olivia Leventhal
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Marian Shahid
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Tim J Nonninger
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Andrew C Yang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Katharina Strempfl
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria.,Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria.,QPS Austria GmbH, Parkring 12, 8074 Grambach, Austria
| | - Michael S Unger
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria.,Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrucken, Germany
| | - Hamilton Oh
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Divya Channappa
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Victor W Henderson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Andreas Keller
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Chair for Clinical Bioinformatics, Saarland University, Saarbrucken, Germany
| | - Ludwig Aigner
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria.,Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Douglas R Galasko
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathleen L Poston
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.,Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
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