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| Status |
Public on May 27, 2024 |
| Title |
Large-scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Many genes are known to regulate Müller glia (MG)-dependent retinal regeneration following widespread tissue damage. Conversely, genes controlling regeneration following limited retinal cell loss, per degenerative disease, are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here, transgenic zebrafish enabling inducible selective retinal ganglion cell (RGC) ablation were combined with single cell multiomics and CRISPR/Cas9-based knockout methods to screen 101 genes for effects on RGC regeneration. We identified 18 regulators of RGC regeneration- seven knockouts inhibited and eleven promoted RGC regeneration. Surprisingly, 35 of 36 known/implicated regulators of retinal tissue regeneration following widespread damage were not required for RGC regeneration, and seven of these knockouts actually enhanced RGC replacement kinetics, including sox2, olig2, and ascl1a. Mechanistic analyses revealed ascl1a knockout increased the propensity of progenitor cells to produce RGCs; i.e., biased progenitor cell fate. These data demonstrate plasticity in how MG can convert to a stem-like state and context-specificity in how genes function during regeneration. Increased understanding of how disease-relevant cell types can be selectively regenerated will, support the development of disease-tailored regenerative therapeutics.
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| Overall design |
We performed single-cell RNA sequencing in larval zebrafish eyes following multiple paradigms of retinal damage including ablation of retinal ganglion cells (RGCs, 4 timepoints) and ablation of rod photoreceptors, and multiome sequencing following ablation of RGCs in fish with the ascl1a gene knocked out via CRISPR/Cas9.
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| Contributor(s) |
Emmerich K, Mumm JS |
| Citation(s) |
39007397 |
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| Submission date |
May 23, 2024 |
| Last update date |
Sep 30, 2024 |
| Contact name |
Kevin Emmerich |
| E-mail(s) |
kemmeri2@jhmi.edu
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| Organization name |
Johns Hopkins University
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| Department |
Ophthalmology
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| Lab |
Jeff Mumm
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| Street address |
1800 Orleans St
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21287 |
| Country |
USA |
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| Platforms (1) |
| GPL24995 |
Illumina NovaSeq 6000 (Danio rerio) |
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| Samples (20)
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| GSM8287433 |
Ablated rod:ntr day 7 48h mtz, replicate 2 |
| GSM8287434 |
Unablated rgc:ntr day 8 |
| GSM8287435 |
Ablated rgc:ntr day 8 48h mtz |
| GSM8287436 |
Unablated rgc:ntr day 7 |
| GSM8287437 |
Ablated rgc:ntr day 7 24h mtz |
| GSM8287438 |
Unablated rgc:ntr day 6 |
| GSM8287439 |
Unablated rgc:ntr day 9 |
| GSM8287440 |
Ablated rgc:ntr day 6 12h mtz |
| GSM8287441 |
Ablated rgc:ntr day 9 72h mtz |
| GSM8287442 |
Multiome rgc:ntr preablation wildtype control day 5 RNA |
| GSM8287443 |
Multiome rgc:ntr preablation ascl1a KO day 5 RNA |
| GSM8287444 |
Multiome rgc:ntr preablation wildtype control day 5 ATAC |
| GSM8287445 |
Multiome rgc:ntr preablation ascl1a KO day 5 ATAC |
| GSM8287446 |
Multiome rgc:ntr 24h ablation wildtype day 7 RNA |
| GSM8287447 |
Multiome rgc:ntr 24h ablation wildtype day 7 ATAC |
| GSM8287448 |
Multiome rgc:ntr 24h ablation ascl1a KO day 7 RNA |
| GSM8287449 |
Multiome rgc:ntr 24h ablation ascl1a KO day 7 ATAC |
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| Relations |
| BioProject |
PRJNA1115053 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE268179_RAW.tar |
990.8 Mb |
(http)(custom) |
TAR (of H5, MTX, TBI, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
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