A Comparative Analysis of Gene and Protein Expression Throughout a Full 28-Day Retinal Regeneration Time-Course in Adult Zebrafish

Abstract

Following photoreceptors ablation by intense light exposure, adult zebrafish are capable of complete regeneration due to the ability of their Müller glia (MG) to re-enter the cell cycle, creating progenitors that differentiate into new photoreceptors. The majority of previous reports on retinal regeneration focused on the first few days of the regenerative response, which include MG cell-cycle re-entry and progenitor cell proliferation. With this study, we analyzed the full 28-day time-course of regeneration by pairing a detailed morphological/immunological analysis with RNA-seq transcriptional profiling at 8 key time points during retinal regeneration. We observed several novel findings. First, we provide evidence for two separate peaks of MG gliosis, with the secondary gliotic peak occurring after MG cell-cycle re-entry. Second, we highlight a distinct transcriptional shift between 5- and 10-days post lesion that highlights the transition from progenitor proliferation to differentiation into new photoreceptors. Third, we show distinctly different patterns of transcriptional recovery of the photoreceptor opsins at 28 days post lesion. Finally, using differential gene expression analysis, we revealed that the established functional recovery of the retina at 28 days post lesion does not, in fact, return to an undamaged transcriptional state, potentially redefining what the field considers complete regeneration. Together, to our knowledge, this work represents the first histological and transcriptomic map of a 28-day time-course of retinal regeneration in adult zebrafish.

Visual Function is Gradually Restored During Retina Regeneration in Adult Zebrafish

“…This phenomenon has already been described together with other regeneration-specific phenotypes including patterning abnormalities in retinal lamination as well as the generation of supernumerary neurons (Fraser et al, 2013;Sherpa et al, 2014;Powell et al, 2016;Ranski et al, 2018). On a molecular level, a recent study described a transcriptional shift from progenitor proliferation to cell differentiation between 5 and 10 days after light lesion (Kramer et al, 2021) which is in line with our observations on structural and functional recovery. They also show that the expression levels of all four opsins and rhodopsin, the photosensitive molecules of the retina, were restored to pre-lesion levels at 10 dpl.…”

Regeneration and Developmental Enhancers Are Differentially Compatible with Minimal Promoters

“…5B, C and Table S2 ). Next, we examined the activities of LEN and 103runx1EN in injured eyes, as lepb and runx1 are both induced upon eye injury (Kramer et al, 2021; Zhao et al, 2014). LEN drove injury-induced expression in the eye when paired with each tested promoter (21%, n=43 for E1b; 49%, n=41 for P0.8 ; 40%, n=35 for P2 ) ( Fig.…”

Regenerative Strategies for Retinal Neurons: Novel Insights in Non-Mammalian Model Organisms

“…Thus, although the restoration of visual performance can be observed already before full morphological recovery of the zebrafish tissue, as expected, both structure and function are crucial steps of the regeneration process because newly regenerated cells must fully integrate into the retinal circuitry. The 28 days’ time-course transcriptomic map of zebrafish retinal degeneration/regeneration was recently described [ 19 ]. This study highlights that the new progenitor cells derived from MG differentiated into new photoreceptors between 5 and 10 days after vision injury.…”

“…Most importantly, the trend of transcriptional recovery of opsins and rhodopsin genes revealed details relevant for the comprehension of regenerative retinal process and future applications. As for instance, it suggests that each cone type, and probably opsins within the same cone (red and green opsins are housed within the same double-cone in zebrafish [ 20 ]), may retain a kinetically distinct differentiation [ 19 ]. To note, 28 days after the lesion, the global transcriptional state did not return to the uninjured condition.…”