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Jacobi A, Tran NM. Defining Selective Neuronal Resilience and Identifying Targets for Neuroprotection and Axon Regeneration Using Single-Cell RNA Sequencing: Experimental Approaches. Methods Mol Biol 2023; 2636:1-18. [PMID: 36881292 DOI: 10.1007/978-1-0716-3012-9_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] [Indexed: 04/14/2023]
Abstract
A prevalent feature among neurodegenerative conditions, including axonal injury, is that certain neuronal types are disproportionately affected, while others are more resilient. Identifying molecular features that separate resilient from susceptible populations could reveal potential targets for neuroprotection and axon regeneration. A powerful approach to resolve molecular differences across cell types is single-cell RNA-sequencing (scRNA-seq). scRNA-seq is a robustly scalable approach that enables the parallel sampling of gene expression across many individual cells. Here we present a systematic framework to apply scRNA-seq to track neuronal survival and gene expression changes following axonal injury. Our methods utilize the mouse retina because it is an experimentally accessible central nervous system tissue and its cell types have been comprehensively characterized by scRNA-seq. This chapter will focus on preparing retinal ganglion cells (RGCs) for scRNA-seq and pre-processing of sequencing results.
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Affiliation(s)
- Anne Jacobi
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicholas M Tran
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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Sood P, Lin A, Yan C, McGillivary R, Diaz U, Makushok T, Nadkarni AV, Tang SKY, Marshall WF. Modular, cascade-like transcriptional program of regeneration in Stentor. eLife 2022; 11:e80778. [PMID: 35924891 PMCID: PMC9371601 DOI: 10.7554/elife.80778] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/04/2022] [Indexed: 11/15/2022] Open
Abstract
The giant ciliate Stentor coeruleus is a classical model system for studying regeneration and morphogenesis in a single cell. The anterior of the cell is marked by an array of cilia, known as the oral apparatus, which can be induced to shed and regenerate in a series of reproducible morphological steps, previously shown to require transcription. If a cell is cut in half, each half regenerates an intact cell. We used RNA sequencing (RNAseq) to assay the dynamic changes in Stentor's transcriptome during regeneration, after both oral apparatus shedding and bisection, allowing us to identify distinct temporal waves of gene expression including kinases, RNA -binding proteins, centriole biogenesis factors, and orthologs of human ciliopathy genes. By comparing transcriptional profiles of different regeneration events, we identified distinct modules of gene expression corresponding to oral apparatus regeneration, posterior holdfast regeneration, and recovery after wounding. By measuring gene expression after blocking translation, we show that the sequential waves of gene expression involve a cascade mechanism in which later waves of expression are triggered by translation products of early-expressed genes. Among the early-expressed genes, we identified an E2F transcription factor and the RNA-binding protein Pumilio as potential regulators of regeneration based on the expression pattern of their predicted target genes. RNAi-mediated knockdown experiments indicate that Pumilio is required for regenerating oral structures of the correct size. E2F is involved in the completion of regeneration but is dispensable for earlier steps. This work allows us to classify regeneration genes into groups based on their potential role for regeneration in distinct cell regeneration paradigms, and provides insight into how a single cell can coordinate complex morphogenetic pathways to regenerate missing structures.
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Affiliation(s)
- Pranidhi Sood
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Athena Lin
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Connie Yan
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Rebecca McGillivary
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Ulises Diaz
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Tatyana Makushok
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Ambika V Nadkarni
- Department of Mechanical Engineering, Stanford UniversityPalo AltoUnited States
| | - Sindy KY Tang
- Department of Mechanical Engineering, Stanford UniversityPalo AltoUnited States
| | - Wallace F Marshall
- Department of Biochemistry & Biophysics, University of California, San FranciscoSan FranciscoUnited States
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Dhara SP, Rau A, Flister MJ, Recka NM, Laiosa MD, Auer PL, Udvadia AJ. Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors. Sci Rep 2019; 9:14198. [PMID: 31578350 PMCID: PMC6775158 DOI: 10.1038/s41598-019-50485-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/10/2019] [Indexed: 11/10/2022] Open
Abstract
In contrast to mammals, adult fish display a remarkable ability to fully regenerate central nervous system (CNS) axons, enabling functional recovery from CNS injury. Both fish and mammals normally undergo a developmental downregulation of axon growth activity as neurons mature. Fish are able to undergo damage-induced “reprogramming” through re-expression of genes necessary for axon growth and guidance, however, the gene regulatory mechanisms remain unknown. Here we present the first comprehensive analysis of gene regulatory reprogramming in zebrafish retinal ganglion cells at specific time points along the axon regeneration continuum from early growth to target re-innervation. Our analyses reveal a regeneration program characterized by sequential activation of stage-specific pathways, regulated by a temporally changing cast of transcription factors that bind to stably accessible DNA regulatory regions. Strikingly, we also find a discrete set of regulatory regions that change in accessibility, consistent with higher-order changes in chromatin organization that mark (1) the beginning of regenerative axon growth in the optic nerve, and (2) the re-establishment of synaptic connections in the brain. Together, these data provide valuable insight into the regulatory logic driving successful vertebrate CNS axon regeneration, revealing key gene regulatory candidates for therapeutic development.
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Affiliation(s)
- Sumona P Dhara
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201, USA
| | - Andrea Rau
- GABI, INRA, AgroParisTech, Universite Paris-Saclay, 78350, Jouy-en-Josas, France.,Joseph J Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201, USA
| | - Michael J Flister
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Nicole M Recka
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201, USA
| | - Michael D Laiosa
- Joseph J Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201, USA
| | - Paul L Auer
- Joseph J Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201, USA
| | - Ava J Udvadia
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201, USA.
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