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Scholz R, Brösamle D, Yuan X, Beyer M, Neher JJ. Epigenetic control of microglial immune responses. Immunol Rev 2024. [PMID: 38491845 DOI: 10.1111/imr.13317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/02/2024] [Indexed: 03/18/2024]
Abstract
Microglia, the major population of brain-resident macrophages, are now recognized as a heterogeneous population comprising several cell subtypes with different (so far mostly supposed) functions in health and disease. A number of studies have performed molecular characterization of these different microglial activation states over the last years making use of "omics" technologies, that is transcriptomics, proteomics and, less frequently, epigenomics profiling. These approaches offer the possibility to identify disease mechanisms, discover novel diagnostic biomarkers, and develop new therapeutic strategies. Here, we focus on epigenetic profiling as a means to understand microglial immune responses beyond what other omics methods can offer, that is, revealing past and present molecular responses, gene regulatory networks and potential future response trajectories, and defining cell subtype-specific disease relevance through mapping non-coding genetic variants. We review the current knowledge in the field regarding epigenetic regulation of microglial identity and function, provide an exemplary analysis that demonstrates the advantages of performing joint transcriptomic and epigenomic profiling of single microglial cells and discuss how comprehensive epigenetic analyses may enhance our understanding of microglial pathophysiology.
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Affiliation(s)
- Rebekka Scholz
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Desirée Brösamle
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Xidi Yuan
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Marc Beyer
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and University of Bonn and West German Genome Center, Bonn, Germany
| | - Jonas J Neher
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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Scholz R, Brösamle D, Yuan X, Neher JJ, Beyer M. Combined Analysis of mRNA Expression and Open Chromatin in Microglia. Methods Mol Biol 2024; 2713:543-571. [PMID: 37639146 DOI: 10.1007/978-1-0716-3437-0_35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
The advance of single-cell RNA-sequencing technologies in the past years has enabled unprecedented insights into the complexity and heterogeneity of microglial cell states in the homeostatic and diseased brain. This includes rather complex proteomic, metabolomic, morphological, transcriptomic, and epigenetic adaptations to external stimuli and challenges resulting in a novel concept of core microglia properties and functions. To uncover the regulatory programs facilitating the rapid transcriptomic adaptation in response to changes in the local microenvironment, the accessibility of gene bodies and gene regulatory elements can be assessed. Here, we describe the application of a previously published method for simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq) on microglia nuclei isolated from frozen mouse brain tissue.
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Affiliation(s)
- Rebekka Scholz
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Desirée Brösamle
- Neuroimmunology and Neurodegenerative Disease, German Center for Neurodegenerative Diseases (DZNE), Tuebingen, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tuebingen, Germany
| | - Xidi Yuan
- Neuroimmunology and Neurodegenerative Disease, German Center for Neurodegenerative Diseases (DZNE), Tuebingen, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tuebingen, Germany
| | - Jonas J Neher
- Neuroimmunology and Neurodegenerative Disease, German Center for Neurodegenerative Diseases (DZNE), Tuebingen, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tuebingen, Germany
| | - Marc Beyer
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
- Platform for Single Cell Genomics and Epigenomics at the University of Bonn and the German Center for Neurodegenerative Diseases, Bonn, Germany.
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Steinbrecher L, Wendeln A, Brösamle D, Liu P, Wild K, Haesler LM, Al‐Shaana R, Neher JJ. The role of microglial HIF‐1α in Aβ pathology. Alzheimers Dement 2020. [DOI: 10.1002/alz.042904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lisa Steinbrecher
- German Center for Neurodegenerative Diseases (DZNE) Tübingen Germany
- Hertie Institute for Clinical Brain Research Tübingen Germany
| | - Ann‐Christin Wendeln
- German Center for Neurodegenerative Diseases (DZNE) Tübingen Germany
- Hertie Institute for Clinical Brain Research Tübingen Germany
| | - Desirée Brösamle
- German Center for Neurodegenerative Diseases (DZNE) Tübingen Germany
- Hertie Institute for Clinical Brain Research Tübingen Germany
| | - Ping Liu
- German Center for Neurodegenerative Diseases (DZNE) Tübingen Germany
- Hertie Institute for Clinical Brain Research Tübingen Germany
| | - Katleen Wild
- German Center for Neurodegenerative Diseases (DZNE) Tübingen Germany
- Hertie Institute for Clinical Brain Research Tübingen Germany
| | - Lisa M. Haesler
- German Center for Neurodegenerative Diseases (DZNE) Tübingen Germany
- Hertie Institute for Clinical Brain Research Tübingen Germany
| | - Rawaa Al‐Shaana
- Hertie Institute for Clinical Brain Research Tübingen Germany
| | - Jonas J. Neher
- German Center for Neurodegenerative Diseases (DZNE) Tübingen Germany
- Hertie Institute for Clinical Brain Research Tübingen Germany
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