Zebrafish as a Translational Model for Eye Development and Repair

An estimated 43.3 million people worldwide are affected by blindness, with cataract, glaucoma, age-related macular degeneration (AMD), and diabetic retinopathy among the leading causes. This growing burden underscores the need for models that enable the identification of potential therapies for these ophthalmic diseases. 

Zebrafish has become a highly relevant vertebrate system for ophthalmic research, not only for studying retinal development but, increasingly, as a platform for discovering therapies that restore visual function after injury.

Mechanisms of Retinal Repair in Zebrafish: Insights From Injury Models

The zebrafish retina is a highly organized, multilayered structure that closely resembles the human retina in both architecture and cell composition. It consists of three main nuclear layers: the outer nuclear layer (ONL), which contains the cell bodies of photoreceptors (rods and cones); the inner nuclear layer (INL), which houses bipolar, horizontal, and amacrine cells as well as Müller glia; and the ganglion cell layer (GCL), which contains the retinal ganglion cells (RGC) whose axons form the optic nerve. These nuclear layers are separated by two synaptic layers: the outer plexiform layer (OPL) and the inner plexiform layer (IPL), where communication between different retinal neurons occurs (Figure 1). 

Zebrafish possess a remarkable ability to regenerate retinal tissue after injury, making them a powerful model for studying neural repair. Unlike mammals, zebrafish can restore all major retinal cell types and recover visual function following various types of retinal damage.

Figure 1. Schematic depicting the different cell types and layers that make up the neural retina in an adult zebrafish. RPE: Pigmented Epithelium; OSL: Outer Segment Layer; ONL: Outer Nuclear Layer; OPL: Outer Plexiform Layer; INL: Inner Nuclear Layer; IPL: Inner Plexiform Layer; RGC: Retinal Ganglion Cells. Source: Zebrafish UCL. 

The central mechanism of retinal repair in zebrafish is the reprogramming of Müller glia, the principal retinal glial cells. Upon injury, these cells de-differentiate, re-enter the cell cycle, and generate multipotent progenitor cells that proliferate and differentiate into all lost retinal neurons. Injury triggers dynamic changes in gene expression and chromatin accessibility in Müller glia, activating networks (e.g., Jak/Stat3, Notch, mTOR, β-catenin) that drive reprogramming and proliferation.

Zebrafish retinal injury can be induced by light damage, chemical toxins, mechanical lesions, or genetic ablation, generating disease models that can be used to screen potential therapeutic compounds in a high-throughput platform. 

Applications of Zebrafish in Preclinical Studies of Regenerative Eye Therapies

Zebrafish are widely used in early-phase preclinical pipelines to identify compounds with restorative potential. Their behavioural assays, particularly the visual-motor response, give rapid feedback on whether structural repair translates into functional improvement. Zebrafish provide a sensitive screening system for evaluating neuroprotective, anti-inflammatory, antiangiogenic, and synapse-stabilizing therapies. Some examples include: 

• Retinal degeneration zebrafish models have been used to evaluate new regenerative agents, such as recombinant human nerve growth factor (rhNGF), which enhance retinal regeneration and functional recovery (Cocchiaro et al. 2022).
• Zebrafish larvae were used to screen a chemical library of 465 drugs to identify small-molecule inhibitors for the hyaloid vasculature angiogenesis. They identified 10 compounds that were able to reduce this abnormal vascular growth in the eye (Merrigan and Kennedy 2017). 
• A retinitis pigmentosa model showed that carvedilol, a beta-blocker, can increase the rod number and improve visual function (Ganzen et al. 2021). 
• A cone photoreceptor degeneration disease model allowed to identify that histone deacetylase 6 inhibitors successfully reduce the number of apoptotic cells and improve the photoreceptor outer segment area and visual function (Sundaramurthi et al. 2020).
• Mutations in EYS are associated with autosomal recessive retinitis pigmentosa (arRP) and autosomal recessive cone-rod dystrophy (arCRD). However, EYS is absent in mouse and rat; thus, zebrafish has become the only relevant model to study the function of EYS in the retina (Lu et al. 2017).

These screenings are only possible when combined with high-resolution imaging and well-defined disease models. At ZeClinics, we have developed zebrafish models for diverse ophthalmic pathologies that include cone-rod dystrophy, diabetic retinopathy, glaucoma, retinitis pigmentosa, Usher syndrome, choroideremia, microphthalmia, and retinal degeneration. 

Our retinal degeneration model clearly illustrates how easily and cost-effectively one can generate meaningful data to evaluate the efficacy of therapies for dry age-related macular degeneration (AMD).

It allows high-throughput screening of compounds with potential capacity to protect from degeneration or enhance regeneration of photoreceptors in the retina. In both cases, the assay starts with adult zebrafish adaptation to complete darkness. For neuroprotective screening, the compound is administered intravitreally before exposing the animals to 60 hours of constant light to induce retinal damage. For pro-repair studies, the order is reversed: the retina is first damaged by light exposure, and the compound is administered afterwards to assess its ability to restore retinal structure or function.

In both cases, cryosections of the eyes are immuno-stained against a photoreceptor marker to evaluate the thickness and cell number of the ONL, the retinal layer populated by rod and cone photoreceptors (Figure 2). 

Figure 2. Neural retina protection assay: retinal cryosections of adult zebrafish eyes immunostained for a photoreceptor marker (red) and nucleus marker (blue). A) NO LID: fish not exposed to constant light (without retinal damage); B) DAMAGED: fish exposed to 60 h LID; C) NEGATIVE CONTROL: fish exposed to 60 h LID upon injection with the vehicle; D) RESCUED: fish exposed to 60 h LID upon injection with an active compound that protects from regeneration. The white bar shows the thickness of the outer nuclear layer (ONL). INL: inner nuclear layer.

Considerations When Using Zebrafish for Ocular Repair Research

While zebrafish are a powerful model for retinal repair, several considerations are essential for designing robust and translationally relevant studies. First, repair in zebrafish occurs within a unique biological context; their innate regenerative capacity and Müller glia responsiveness differ from the more limited regenerative environment of the human retina. For drug discovery focused on repair rather than full regeneration, selecting the appropriate injury severity and time window is critical to avoid misinterpreting regenerative phenomena as pharmacological effects.

On another note, behavioural readouts need to be complemented with structural and molecular endpoints to ensure that improvements reflect true repair rather than temporary compensation. Integrating functional assays with detailed histological analysis provides a clearer view of how a compound acts. 

At ZeClinics, we combine histological analysis with well-described behavioural features, such as the prey consumption assay. Feeding behavior in zebrafish larvae depends on an intact ocular system. If vision is impaired, hunting rotifers becomes harder. If the tested candidate works and repairs the ocular defect, the rotifers' consumption increases. 

This test is a simple assay with lots of biological power: 

1.  At 7 days post-fertilization, each larva is placed in a well with 100 rotifers.
2. After 3.5 hours, we quantify how many remain using computational image analysis.
3. The result is a quantitative readout of visual performance across mutant, heterozygous, and wild-type groups, with and without treatment.

Ultimately, model selection should align with the intended clinical indication. For example, light-induced degeneration is particularly suitable for photoreceptor-targeted therapies. Aligning the model with the disease biology ensures that drug effects are meaningful and predictive of later-stage outcomes.

Although some limitations remain, zebrafish provide an efficient and biologically relevant system for identifying compounds that promote retinal repair. Their versatility makes them a valuable component of modern ophthalmic drug discovery pipelines and an important bridge between molecular research and translational medicine.

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References

Cerveny K. Retina [Internet]. London: Zebrafish UCL; [cited 2025 Dec 4]. Available from: https://zebrafishucl.org/retina

Cocchiaro P, Di Donato V, Rubbini D, Mastropasqua R, Allegretti M, Mantelli F, Aramini A, Brandolini L. Intravitreal Administration of rhNGF Enhances Regenerative Processes in a Zebrafish Model of Retinal Degeneration. Front Pharmacol. 2022 Mar 7;13:822359. doi: 10.3389/fphar.2022.822359.

Ganzen L, Venkatraman P, Pang CP, Leung YF, Zhang M. Utilizing Zebrafish Visual Behaviors in Drug Screening for Retinal Degeneration. Int J Mol Sci. 2017 Jun 2;18(6):1185. doi: 10.3390/ijms18061185.

Hong Y, Luo Y. Zebrafish Model in Ophthalmology to Study Disease Mechanism and Drug Discovery. Pharmaceuticals (Basel). 2021 Jul 25;14(8):716. doi: 10.3390/ph14080716.

Lu Z, Hu X, Liu F, Soares DC, Liu X, Yu S, Gao M, Han S, Qin Y, Li C, Jiang T, Luo D, Guo A-Y, Tang Z, Liu M. Ablation of EYS in zebrafish causes mislocalisation of outer segment proteins, F-actin disruption and cone-rod dystrophy. Sci Rep. 2017; 7: 46098. doi:10.1038/srep46098

Merrigan SL, Kennedy BN. Vitamin D receptor agonists regulate ocular developmental angiogenesis and modulate expression of dre-miR-21 and VEGF. Br J Pharmacol. 2017 Aug;174(16):2636-2651. doi: 10.1111/bph.13875. 

Sundaramurthi H, Roche SL, Grice GL, Moran A, Dillion ET, Campiani G, Nathan JA, Kennedy BN. Selective Histone Deacetylase 6 Inhibitors Restore Cone Photoreceptor Vision or Outer Segment Morphology in Zebrafish and Mouse Models of Retinal Blindness. Front Cell Dev Biol. 2020 Aug 26;8:689. doi: 10.3389/fcell.2020.00689.

By Miriam Martínez

Miriam is a Human Biologist with a strong background in neuropharmacology and a passion for bridging science and innovation. After earning a master’s degree in the Pharmaceutical and Biotech Industry, she completed her PhD in Biomedicine at Pompeu Fabra University (Barcelona), where her research focused on the behavioral analysis of animal models for neurophenotypical characterization. Following her doctoral studies, Miriam transitioned into the healthcare marketing and communication sector, where she played a key role in developing impactful marketing strategies and educational campaigns for leading pharmaceutical brands. She now leverages her scientific expertise, strategic thinking, and creative communication skills in her current role at ZeClinics.