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Lam M, Lee D, Kosater I, Khairallah A, Taga M, Zhang Y, Fujita M, Nag S, Bennett DA, De Jager P, Menon V. Human disease-specific cell signatures in non-lesional tissue in Multiple Sclerosis detected by single-cell and spatial transcriptomics. bioRxiv 2023:2023.12.20.572491. [PMID: 38187779 PMCID: PMC10769298 DOI: 10.1101/2023.12.20.572491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Recent investigations of cell type changes in Multiple Sclerosis (MS) using single-cell profiling methods have focused on active lesional and peri-lesional brain tissue, and have implicated a number of peripheral and central nervous system cell types. However, an important question is the extent to which so-called "normal-appearing" non-lesional tissue in individuals with MS accumulate changes over the lifespan. Here, we compared post-mortem non-lesional brain tissue from donors with a pathological or clinical diagnosis of MS from the Religious Orders Study or Rush Memory and Aging Project (ROSMAP) cohorts to age- and sex-matched brains from persons without MS (controls). We profiled three brain regions using single-nucleus RNA-seq: dorsolateral prefrontal cortex (DLPFC), normal appearing white matter (NAWM) and the pulvinar in thalamus (PULV), from 15 control individuals, 8 individuals with MS, and 5 individuals with other detrimental pathologies accompanied by demyelination, resulting in a total of 78 samples. We identified region- and cell type-specific differences in non-lesional samples from individuals diagnosed with MS and/or exhibiting secondary demyelination with other neurological conditions, as compared to control donors. These differences included lower proportions of oligodendrocytes with expression of myelination related genes MOBP, MBP, PLP1, as well as higher proportions of CRYAB+ oligodendrocytes in all three brain regions. Among microglial signatures, we identified subgroups that were higher in both demyelination (TMEM163+/ERC2+), as well as those that were specifically higher in MS donors (HIF1A+/SPP1+) and specifically in donors with secondary demyelination (SOCS6+/MYO1E+), in both white and grey matter. To validate our findings, we generated Visium spatial transcriptomics data on matched tissue from 13 donors, and recapitulated our observations of gene expression differences in oligodendrocytes and microglia. Finally, we show that some of the differences observed between control and MS donors in NAWM mirror those previously reported between control WM and active lesions in MS donors. Overall, our investigation sheds additional light on cell type- and disease-specific differences present even in non-lesional white and grey matter tissue, highlighting widespread cellular signatures that may be associated with downstream pathological changes.
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Affiliation(s)
- Matti Lam
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Dylan Lee
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Ivy Kosater
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Anthony Khairallah
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Mariko Taga
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Ya Zhang
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Masashi Fujita
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Sukriti Nag
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL
| | - Philip De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center
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Olah M, Menon V, Habib N, Taga MF, Ma Y, Yung CJ, Cimpean M, Khairallah A, Coronas-Samano G, Sankowski R, Grün D, Kroshilina AA, Dionne D, Sarkis RA, Cosgrove GR, Helgager J, Golden JA, Pennell PB, Prinz M, Vonsattel JPG, Teich AF, Schneider JA, Bennett DA, Regev A, Elyaman W, Bradshaw EM, De Jager PL. Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer's disease. Nat Commun 2020; 11:6129. [PMID: 33257666 PMCID: PMC7704703 DOI: 10.1038/s41467-020-19737-2] [Citation(s) in RCA: 313] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 10/26/2020] [Indexed: 01/05/2023] Open
Abstract
The extent of microglial heterogeneity in humans remains a central yet poorly explored question in light of the development of therapies targeting this cell type. Here, we investigate the population structure of live microglia purified from human cerebral cortex samples obtained at autopsy and during neurosurgical procedures. Using single cell RNA sequencing, we find that some subsets are enriched for disease-related genes and RNA signatures. We confirm the presence of four of these microglial subpopulations histologically and illustrate the utility of our data by characterizing further microglial cluster 7, enriched for genes depleted in the cortex of individuals with Alzheimer's disease (AD). Histologically, these cluster 7 microglia are reduced in frequency in AD tissue, and we validate this observation in an independent set of single nucleus data. Thus, our live human microglia identify a range of subtypes, and we prioritize one of these as being altered in AD.
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Affiliation(s)
- Marta Olah
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Naomi Habib
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
- Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mariko F Taga
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Yiyi Ma
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Christina J Yung
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
| | - Maria Cimpean
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
| | - Anthony Khairallah
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
| | - Guillermo Coronas-Samano
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Roman Sankowski
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
- Berta-Ottenstein-Programme for Clinician Scientists, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominic Grün
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Alexandra A Kroshilina
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
| | | | - Rani A Sarkis
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Garth R Cosgrove
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeffrey Helgager
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeffrey A Golden
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Page B Pennell
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Marco Prinz
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Center for NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jean Paul G Vonsattel
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Andrew F Teich
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Aviv Regev
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA, 02140, USA
- Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Wassim Elyaman
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Elizabeth M Bradshaw
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA.
- Department of Neurology, Columbia University Medical Center, New York, NY, USA.
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA.
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Taga M, Petyuk VA, White C, Marsh G, Ma Y, Klein HU, Connor SM, Kroshilina A, Yung CJ, Khairallah A, Olah M, Schneider J, Karhohs K, Carpenter AE, Ransohoff R, Bennett DA, Crotti A, Bradshaw EM, De Jager PL. BIN1 protein isoforms are differentially expressed in astrocytes, neurons, and microglia: neuronal and astrocyte BIN1 are implicated in tau pathology. Mol Neurodegener 2020; 15:44. [PMID: 32727516 PMCID: PMC7389646 DOI: 10.1186/s13024-020-00387-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 06/08/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Identified as an Alzheimer's disease (AD) susceptibility gene by genome wide-association studies, BIN1 has 10 isoforms that are expressed in the Central Nervous System (CNS). The distribution of these isoforms in different cell types, as well as their role in AD pathology still remains unclear. METHODS Utilizing antibodies targeting specific BIN1 epitopes in human post-mortem tissue and analyzing mRNA expression data from purified microglia, we identified three isoforms expressed in neurons and astrocytes (isoforms 1, 2 and 3) and four isoforms expressed in microglia (isoforms 6, 9, 10 and 12). The abundance of selected peptides, which correspond to groups of BIN1 protein isoforms, was measured in dorsolateral prefrontal cortex, and their relation to neuropathological features of AD was assessed. RESULTS Peptides contained in exon 7 of BIN1's N-BAR domain were found to be significantly associated with AD-related traits and, particularly, tau tangles. Decreased expression of BIN1 isoforms containing exon 7 is associated with greater accumulation of tangles and subsequent cognitive decline, with astrocytic rather than neuronal BIN1 being the more likely culprit. These effects are independent of the BIN1 AD risk variant. CONCLUSIONS Exploring the molecular mechanisms of specific BIN1 isoforms expressed by astrocytes may open new avenues for modulating the accumulation of Tau pathology in AD.
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Affiliation(s)
- Mariko Taga
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
| | | | - Charles White
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
| | | | - Yiyi Ma
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
| | - Sarah M. Connor
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
| | - Alexandra Kroshilina
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
| | - Christina J. Yung
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
| | - Anthony Khairallah
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
| | - Marta Olah
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
| | - Julie Schneider
- Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL USA
| | - Kyle Karhohs
- Imaging Platform, Broad Institute, Cambridge, MA USA
| | | | - Richard Ransohoff
- Third Rock Ventures, 29 Newbury Street, Suite 301, Boston, MA 02116 USA
- Department of Cell Biology, Harvard Medical School, Boston, MA USA
| | - David A. Bennett
- Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL USA
| | | | - Elizabeth M. Bradshaw
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
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