Transcriptomic comparison of two selective retinal cell ablation paradigms in zebrafish reveals shared and cell-specific regenerative responses

Retinal Müller glia (MG) can act as stem-like cells to generate new neurons in both zebrafish and 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 responses underlying regeneration following targeted loss of rod photoreceptors or bipolar cells. In total, 2,531 differentially expressed genes (DEGs) were identified, with the majority being paradigm specific, including during early 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 and components of JAK/STAT signaling were implicated in both paradigms. To examine candidate gene roles in rod cell regeneration, including several immune-related factors, CRISPR/Cas9 was used to create G0 mutant larvae (i.e., “crispants”). Rod cell regeneration was inhibited in stat3 crispants, while mutating stat5a/b, c7b and txn accelerated rod regeneration kinetics. These data support emerging evidence that discrete responses follow from selective retinal cell loss and that the immune system plays a key role in regulating “fate-biased” regenerative processes. Author Summary Blinding diseases are linked to the loss of specific types of neurons in the retina. In humans, this eventually leads to loss of sight. In zebrafish, however, lost retinal neurons are regenerated resulting in restored vision. Our lab has developed zebrafish models that induce the loss of disease-relevant retinal neurons, thereby allowing us to study how individual cell types are regenerated. Here, to better understand how these processes are regulated, we compared gene expression changes occurring during loss and regeneration of two different retinal cell types, rod photoreceptors and bipolar interneurons. The majority of gene changes were specific to each cell type studied, providing strong evidence that genetic programs underlying stem cell activation vary depending on the cell type lost. We also found that the immune system was implicated as a regulator of regeneration in both models, but that individual immune-related genes were more strongly associated with one of the two models. Furthermore, disrupting multiple genes involved in immune system signaling led to enhanced rod regeneration. We hope that a better understanding of how retinal cell regeneration is regulated in zebrafish will aid efforts to develop regenerative therapeutics designed to restore sight to patients who have lost their vision.