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Holmberg JC, Riley VA, Sokolov AM, Mukherjee S, Feliciano DM. Protocol for electroporating and isolating murine (sub)ventricular zone cells for single-nuclei omics. STAR Protoc 2024; 5:103095. [PMID: 38823010 DOI: 10.1016/j.xpro.2024.103095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/14/2024] [Accepted: 05/08/2024] [Indexed: 06/03/2024] Open
Abstract
In vivo genetic modification of neural stem cells is necessary to model the origins and pathogenesis of neurological disorders. Electroporation is a technique that applies a transient electrical field to direct charged molecules into living cells to genetically modify the mouse brain. Here, we provide a protocol to electroporate the neural stem cells surrounding the neonatal ventricles. We describe subsequent steps to isolate and prepare nuclei from the cells and their cellular progeny for single-nuclei omics. For complete details on the use and execution of this protocol, please refer to Riley et al.1.
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Affiliation(s)
- Jennie C Holmberg
- Department of Biological Sciences, Clemson University, Clemson, SC 29631, USA.
| | - Victoria A Riley
- Department of Biological Sciences, Clemson University, Clemson, SC 29631, USA
| | - Aidan M Sokolov
- Department of Biological Sciences, Clemson University, Clemson, SC 29631, USA
| | - Sulagna Mukherjee
- Department of Biological Sciences, Clemson University, Clemson, SC 29631, USA
| | - David M Feliciano
- Department of Biological Sciences, Clemson University, Clemson, SC 29631, USA; Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA.
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2
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Butto T, Chongtham MC, Mungikar K, Hartwich D, Linke M, Ruffini N, Radyushkin K, Schweiger S, Winter J, Gerber S. Characterization of transcriptional profiles associated with stress-induced neuronal activation in Arc-GFP mice. Mol Psychiatry 2024:10.1038/s41380-024-02555-z. [PMID: 38649752 DOI: 10.1038/s41380-024-02555-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/21/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024]
Abstract
Chronic stress has become a predominant factor associated with a variety of psychiatric disorders, such as depression and anxiety, in both human and animal models. Although multiple studies have looked at transcriptional changes after social defeat stress, these studies primarily focus on bulk tissues, which might dilute important molecular signatures of social interaction in activated cells. In this study, we employed the Arc-GFP mouse model in conjunction with chronic social defeat (CSD) to selectively isolate activated nuclei (AN) populations in the ventral hippocampus (vHIP) and prefrontal cortex (PFC) of resilient and susceptible animals. Nuclear RNA-seq of susceptible vs. resilient populations revealed distinct transcriptional profiles linked predominantly with neuronal and synaptic regulation mechanisms. In the vHIP, susceptible AN exhibited increased expression of genes related to the cytoskeleton and synaptic organization. At the same time, resilient AN showed upregulation of cell adhesion genes and differential expression of major glutamatergic subunits. In the PFC, susceptible mice exhibited upregulation of synaptotagmins and immediate early genes (IEGs), suggesting a potentially over-amplified neuronal activity state. Our findings provide a novel view of stress-exposed neuronal activation and the molecular response mechanisms in stress-susceptible vs. resilient animals, which may have important implications for understanding mental resilience.
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Affiliation(s)
- Tamer Butto
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, 55128, Mainz, Germany
| | | | - Kanak Mungikar
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Dewi Hartwich
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Matthias Linke
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Nicolas Ruffini
- Leibniz Institute for Resilience Research, Wallstr 7, 55122, Mainz, Germany
| | | | - Susann Schweiger
- Leibniz Institute for Resilience Research, Wallstr 7, 55122, Mainz, Germany
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Jennifer Winter
- Leibniz Institute for Resilience Research, Wallstr 7, 55122, Mainz, Germany.
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany.
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany.
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3
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Soule TG, Pontifex CS, Rosin N, Joel MM, Lee S, Nguyen MD, Chhibber S, Pfeffer G. A protocol for single nucleus RNA-seq from frozen skeletal muscle. Life Sci Alliance 2023; 6:e202201806. [PMID: 36914268 PMCID: PMC10011611 DOI: 10.26508/lsa.202201806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Single-cell technologies are a method of choice to obtain vast amounts of cell-specific transcriptional information under physiological and diseased states. Myogenic cells are resistant to single-cell RNA sequencing because of their large, multinucleated nature. Here, we report a novel, reliable, and cost-effective method to analyze frozen human skeletal muscle by single-nucleus RNA sequencing. This method yields all expected cell types for human skeletal muscle and works on tissue frozen for long periods of time and with significant pathological changes. Our method is ideal for studying banked samples with the intention of studying human muscle disease.
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Affiliation(s)
- Tyler Gb Soule
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Carly S Pontifex
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Nicole Rosin
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Matthew M Joel
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Sukyoung Lee
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Minh Dang Nguyen
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Sameer Chhibber
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Gerald Pfeffer
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
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4
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Miranda AMA, Janbandhu V, Maatz H, Kanemaru K, Cranley J, Teichmann SA, Hübner N, Schneider MD, Harvey RP, Noseda M. Single-cell transcriptomics for the assessment of cardiac disease. Nat Rev Cardiol 2023; 20:289-308. [PMID: 36539452 DOI: 10.1038/s41569-022-00805-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/03/2022] [Indexed: 12/24/2022]
Abstract
Cardiovascular disease is the leading cause of death globally. An advanced understanding of cardiovascular disease mechanisms is required to improve therapeutic strategies and patient risk stratification. State-of-the-art, large-scale, single-cell and single-nucleus transcriptomics facilitate the exploration of the cardiac cellular landscape at an unprecedented level, beyond its descriptive features, and can further our understanding of the mechanisms of disease and guide functional studies. In this Review, we provide an overview of the technical challenges in the experimental design of single-cell and single-nucleus transcriptomics studies, as well as a discussion of the type of inferences that can be made from the data derived from these studies. Furthermore, we describe novel findings derived from transcriptomics studies for each major cardiac cell type in both health and disease, and from development to adulthood. This Review also provides a guide to interpreting the exhaustive list of newly identified cardiac cell types and states, and highlights the consensus and discordances in annotation, indicating an urgent need for standardization. We describe advanced applications such as integration of single-cell data with spatial transcriptomics to map genes and cells on tissue and define cellular microenvironments that regulate homeostasis and disease progression. Finally, we discuss current and future translational and clinical implications of novel transcriptomics approaches, and provide an outlook of how these technologies will change the way we diagnose and treat heart disease.
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Affiliation(s)
| | - Vaibhao Janbandhu
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Henrike Maatz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Kazumasa Kanemaru
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - James Cranley
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sarah A Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Deptartment of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Charite-Universitätsmedizin Berlin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | | | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK.
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5
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Butto T, Mungikar K, Baumann P, Winter J, Lutz B, Gerber S. Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing. Cells 2023; 12:cells12071051. [PMID: 37048124 PMCID: PMC10093037 DOI: 10.3390/cells12071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
In the last decade, we have witnessed an upsurge in nuclei-based studies, particularly coupled with next-generation sequencing. Such studies aim at understanding the molecular states that exist in heterogeneous cell populations by applying increasingly more affordable sequencing approaches, in addition to optimized methodologies developed to isolate and select nuclei. Although these powerful new methods promise unprecedented insights, it is important to understand and critically consider the associated challenges. Here, we provide a comprehensive overview of the rise of nuclei-based studies and elaborate on their advantages and disadvantages, with a specific focus on their utility for transcriptomic sequencing analyses. Improved designs and appropriate use of the various experimental strategies will result in acquiring biologically accurate and meaningful information.
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Affiliation(s)
- Tamer Butto
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, 55128 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
| | - Kanak Mungikar
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
| | - Peter Baumann
- Faculty of Biology, Johannes Gutenberg-University, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Jennifer Winter
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
| | - Beat Lutz
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
- Institute of Physiological Chemistry, University Medical Center Mainz, 55128 Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
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6
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Cell-type specific profiling of histone post-translational modifications in the adult mouse striatum. Nat Commun 2022; 13:7720. [PMID: 36513652 PMCID: PMC9747932 DOI: 10.1038/s41467-022-35384-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022] Open
Abstract
Epigenetic gene regulation in the heterogeneous brain remains challenging to decipher with current strategies. Bulk tissue analysis from pooled subjects reflects the average of cell-type specific changes across cell-types and individuals, which obscures causal relationships between epigenetic modifications, regulation of gene expression, and complex pathology. To address these limitations, we optimized a hybrid protocol, ICuRuS, for the isolation of nuclei tagged in specific cell-types and histone post translational modification profiling from the striatum of a single mouse. We combined affinity-based isolation of the medium spiny neuron subtypes, Adenosine 2a Receptor or Dopamine Receptor D1, with cleavage of histone-DNA complexes using an antibody-targeted micrococcal nuclease to release DNA complexes for paired end sequencing. Unlike fluorescence activated cell sorting paired with chromatin immunoprecipitation, ICuRuS allowed for robust epigenetic profiling at cell-type specific resolution. Our analysis provides a framework to understand combinatorial relationships between neuronal-subtype-specific epigenetic modifications and gene expression.
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7
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Somatic copy number variant load in neurons of healthy controls and Alzheimer's disease patients. Acta Neuropathol Commun 2022; 10:175. [PMID: 36451207 PMCID: PMC9714068 DOI: 10.1186/s40478-022-01452-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/27/2022] [Indexed: 12/03/2022] Open
Abstract
The possible role of somatic copy number variations (CNVs) in Alzheimer's disease (AD) aetiology has been controversial. Although cytogenetic studies suggested increased CNV loads in AD brains, a recent single-cell whole-genome sequencing (scWGS) experiment, studying frontal cortex brain samples, found no such evidence. Here we readdressed this issue using low-coverage scWGS on pyramidal neurons dissected via both laser capture microdissection (LCM) and fluorescence activated cell sorting (FACS) across five brain regions: entorhinal cortex, temporal cortex, hippocampal CA1, hippocampal CA3, and the cerebellum. Among reliably detected somatic CNVs identified in 1301 cells obtained from the brains of 13 AD patients and 7 healthy controls, deletions were more frequent compared to duplications. Interestingly, we observed slightly higher frequencies of CNV events in cells from AD compared to similar numbers of cells from controls (4.1% vs. 1.4%, or 0.9% vs. 0.7%, using different filtering approaches), although the differences were not statistically significant. On the technical aspects, we observed that LCM-isolated cells show higher within-cell read depth variation compared to cells isolated with FACS. To reduce within-cell read depth variation, we proposed a principal component analysis-based denoising approach that significantly improves signal-to-noise ratios. Lastly, we showed that LCM-isolated neurons in AD harbour slightly more read depth variability than neurons of controls, which might be related to the reported hyperploid profiles of some AD-affected neurons.
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8
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Resilience and the Gut Microbiome: Insights from Chronically Socially Stressed Wild-Type Mice. Microorganisms 2022; 10:microorganisms10061077. [PMID: 35744594 PMCID: PMC9231072 DOI: 10.3390/microorganisms10061077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/12/2022] [Accepted: 05/19/2022] [Indexed: 12/12/2022] Open
Abstract
The microbiome is an important player within physiological homeostasis of the body but also in pathophysiological derailments. Chronic social stress is a challenge to the organism, which results in psychological illnesses such as depression in some individuals and can be counterbalanced by others, namely resilient individuals. In this study, we wanted to elucidate the potential contribution of the microbiome to promote resilience. Male mice were subjected to the classical chronic social defeat paradigm. Defeated or undefeated mice were either controls (receiving normal drinking water) or pre-treated with antibiotics or probiotics. Following social defeat, resilient behavior was assessed by means of the social interaction test. Neither depletion nor probiotic-shifted alteration of the microbiome influenced stress-associated behavioral outcomes. Nevertheless, clear changes in microbiota composition due to the defeat stress were observed such as elevated Bacteroides spp. This stress-induced increase in Bacteroides in male mice could be confirmed in a related social stress paradigm (instable social hierarchy) in females. This indicates that while manipulation of the microbiome via the antibiotics- and probiotics-treatment regime used here has no direct impact on modulating individual stress susceptibility in rodents, it clearly affects the microbiome in the second line and in a sex-independent manner regarding Bacteroides.
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9
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Pena-Ortiz MA, Shafiq S, Rowland ME, Bérubé NG. Selective isolation of mouse glial nuclei optimized for reliable downstream omics analyses. J Neurosci Methods 2022; 369:109480. [PMID: 35026308 DOI: 10.1016/j.jneumeth.2022.109480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND Isolation of cell types of interest from the brain for molecular applications presents several challenges, including cellular damage during tissue dissociation or enrichment procedures, and low cell number in the tissue in some cases. Techniques have been developed to enrich distinct cell populations using immunopanning or fluorescence activated cell/nuclei sorting. However, these techniques often involve fixation, immunolabeling and DNA staining steps, which could potentially influence downstream omics applications. NEW METHOD Taking advantage of readily available genetically modified mice with fluorescent-tagged nuclei, we describe a technique for the purification of cell-type specific brain nuclei, optimized to decrease sample preparation time and to limit potential artefacts for downstream omics applications. We demonstrate the applicability of this approach for the purification of glial cell nuclei and show that the resulting cell-type specific nuclei obtained can be used effectively for omics applications, including ATAC-seq and RNA-seq. RESULTS We demonstrate excellent enrichment of fluorescently-tagged glial nuclei, yielding high quality RNA and chromatin. We identify several critical steps during nuclei isolation that help limit nuclei rupture and clumping, including quick homogenization, dilution before filtration and loosening of the pellet before resuspension, thus improving yield. Sorting of fluorescent nuclei can be achieved without fixation, antibody labelling, or DAPI staining, reducing potential artifactual results in RNA-seq and ATAC-seq analyses. We show that reproducible glial cell type-specific profiles can be obtained in transcriptomic and chromatin accessibility assays using this rapid protocol. COMPARISON WITH EXISTING METHODS Our method allows for rapid enrichment of glial nuclei populations from the mouse brain with minimal processing steps, while still providing high quality RNA and chromatin required for reliable omics analyses. CONCLUSIONS We provide a reproducible method to obtain nucleic material from glial cells in the mouse brain with a quick and limited sample preparation.
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Affiliation(s)
- Miguel A Pena-Ortiz
- Departments of Anatomy and Cell Biology, Paediatrics, and Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada; Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada
| | - Sarfraz Shafiq
- Departments of Anatomy and Cell Biology, Paediatrics, and Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada; Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada
| | - Megan E Rowland
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Nathalie G Bérubé
- Departments of Anatomy and Cell Biology, Paediatrics, and Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada; Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada.
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10
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Guan PP, Cao LL, Yang Y, Wang P. Calcium Ions Aggravate Alzheimer's Disease Through the Aberrant Activation of Neuronal Networks, Leading to Synaptic and Cognitive Deficits. Front Mol Neurosci 2021; 14:757515. [PMID: 34924952 PMCID: PMC8674839 DOI: 10.3389/fnmol.2021.757515] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/04/2021] [Indexed: 12/11/2022] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease that is characterized by the production and deposition of β-amyloid protein (Aβ) and hyperphosphorylated tau, leading to the formation of β-amyloid plaques (APs) and neurofibrillary tangles (NFTs). Although calcium ions (Ca2+) promote the formation of APs and NFTs, no systematic review of the mechanisms by which Ca2+ affects the development and progression of AD has been published. Therefore, the current review aimed to fill the gaps between elevated Ca2+ levels and the pathogenesis of AD. Specifically, we mainly focus on the molecular mechanisms by which Ca2+ affects the neuronal networks of neuroinflammation, neuronal injury, neurogenesis, neurotoxicity, neuroprotection, and autophagy. Furthermore, the roles of Ca2+ transporters located in the cell membrane, endoplasmic reticulum (ER), mitochondria and lysosome in mediating the effects of Ca2+ on activating neuronal networks that ultimately contribute to the development and progression of AD are discussed. Finally, the drug candidates derived from herbs used as food or seasoning in Chinese daily life are summarized to provide a theoretical basis for improving the clinical treatment of AD.
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Affiliation(s)
- Pei-Pei Guan
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Long-Long Cao
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Yi Yang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Pu Wang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
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11
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Blackmore M, Batsel E, Tsoulfas P. Widening spinal injury research to consider all supraspinal cell types: Why we must and how we can. Exp Neurol 2021; 346:113862. [PMID: 34520726 PMCID: PMC8805209 DOI: 10.1016/j.expneurol.2021.113862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/19/2021] [Accepted: 09/08/2021] [Indexed: 01/05/2023]
Abstract
The supraspinal connectome consists of dozens of neuronal populations that project axons from the brain to the spinal cord to influence a wide range of motor, autonomic, and sensory functions. The complexity and wide distribution of supraspinal neurons present significant technical challenges, leading most spinal cord injury research to focus on a handful of major pathways such as the corticospinal, rubrospinal, and raphespinal. Much less is known about many additional populations that carry information to modulate or compensate for these main pathways, or which carry pre-autonomic and other information of high value to individuals with spinal injury. A confluence of technical developments, however, now enables a whole-connectome study of spinal cord injury. Improved viral labeling, tissue clearing, and automated registration to 3D atlases can quantify supraspinal neurons throughout the murine brain, offering a practical means to track responses to injury and treatment on an unprecedented scale. Here we discuss the need for expanded connectome-wide analyses in spinal injury research, illustrate the potential by discussing a new web-based resource for brain-wide study of supraspinal neurons, and highlight future prospects for connectome analyses.
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Affiliation(s)
- Murray Blackmore
- Department of Biomedical Sciences, Marquette University, 53201, United States of America.
| | - Elizabeth Batsel
- Department of Biomedical Sciences, Marquette University, 53201, United States of America
| | - Pantelis Tsoulfas
- Department of Neurological Surgery, Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL 33136, United States of America
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