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Large-scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific

ABSTRACT: 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.

ORGANISM(S): Danio rerio

PROVIDER: GSE268179 | GEO | 2024/05/27

REPOSITORIES: GEO

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Project description:Retinal Müller glia (MG) can act as stem-like cells to generate new neurons in both zebrafish in mice. In zebrafish, retinal regeneration is innate and robust, resulting in the replacement of lost neurons and restoration of visual function. In mice, exogenous stimulation of MG is required to reveal a dormant and, to date, limited regenerative capacity. Zebrafish studies have been key in revealing factors that promote regenerative responses in the mammalian eye. Increased understanding of how the regenerative potential of MG is regulated in zebrafish may therefore aid efforts to promote retinal repair therapeutically. Developmental signaling pathways are known to coordinate regeneration following widespread retinal cell loss. In contrast, less is known about how regeneration is regulated in the context of retinal degenerative disease, i.e., following the loss of specific retinal cell types. To address this knowledge gap, we compared transcriptomic changes between two selective cell ablation paradigms, targeted loss of rod photoreceptors or bipolar cells. Our study spanned twelve time points encompassing the entire degenerative and regenerative process of each targeted cell type. 2,531 differentially expressed genes (DEGs) were identified. Interestingly, the majority of DEGs were paradigm specific, including during MG activation phases, suggesting the nature of the injury/cell loss informs the regenerative process from initiation onward. For example, early modulation of Notch signaling was implicated in the rod but not bipolar cell ablation paradigm. Components of JAK/STAT signaling were activated in both paradigms but were more strongly induced during rod cell regeneration. We functionally validated the role of JAK/STAT signaling during rod cell regeneration using CRISPR/Cas9-based knockdown of stat3 which inhibited both MG proliferation and rod cell regeneration kinetics. Additionally, although more than a third of all DEGs are implicated as immune-system regulators, individual immune-related factors were largely paradigm specific. These data support emerging evidence that discrete “fate-biased” regenerative processes follow from selective retinal cell loss. Microarrays were used to follow gene expression changes in the eyes of fish following either rod or bipolar specific induced death.

Project description:To investigate the retinal proteins associated with primary and secondary retinal ganglion cell (RGC) degeneration and explore their molecular pathways, SWATH label-free and target-based mass spectrometry was employed to identify the proteomes in various retinal locations in response to localized optic nerve injury. Unilateral partial optic nerve transection (pONT) was performed on adult Wistar rats and their retinas were harvested at 2 weeks later. To confirm the separation of primary and secondary RGC degeneration, immunohistochemistry of RNA binding protein with multiple splicing (RBPMS) and glial fibrillary acidic protein (GFAP) was performed on retinal whole-mounts. Retinal proteomes in the temporal and nasal quadrants were evaluated with high resolution hybrid quadrupole time-of-flight mass spectrometry (QTOF-MS), and SWATH-based acquisition, and their expression was compared to the corresponding retinal quadrant in contralateral control eyes and further validated by multiple reaction monitoring mass spectrometry (MRM-MS). A total of 3641 proteins (p<0.05, FDR<1%) were quantified by SWATH-MS. Bioinformatics data analysis showed that there were 35 up-regulated and 24 down-regulated proteins in the temporal quadrant while 19 and 5 proteins were up-regulated and down-regulated, respectively, in the nasal quadrant respectively (n=4, p<0.05; fold change ≥1.4 fold or ≤0.7). Six proteins were regulated in both the temporal and the nasal quadrants including CLU, GFAP, GNG5, IRF2BPL, L1CAM and CPLX1. Linear regression analysis indicated a strong association between the data obtained by SWATH-MS and MRM-MS (temporal, R2=0.97; nasal, R2=0.96). Gene ontology analysis reveals statistically significant changes in the biological processes and cellular components of primary RGC degeneration. The majority of the significant changes in structural, signaling, and cell death proteins were associated with loss of RGCs in the area of primary RGC degeneration. The combined use of SWATH-MS and MRM-MS methods detects and quantifies regional changes of retinal protein expressions after localized injury. Future investigation with this integrated approach will significantly increase understanding of diverse processes of progressive RGC degeneration from a proteomic prospective.

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Large-scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific

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