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Published on: January 12, 2015
Comparative analysis of transcriptional changes in zebrafish
Sarah E Grabinski1, Dhwani Parsana1, Brian D Perkins1,2,3
1Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, United States.
Abstract:
Acute injury to the adult zebrafish retina triggers the release of pro-inflammatory cytokines and growth factors that stimulate multiple gene regulatory networks, which ultimately stimulate Müller glia to proliferate and regenerate neurons. In contrast, zebrafish carrying mutations in cep290 or bbs2 undergo progressive loss of cone photoreceptors and exhibit signs of microglia activation and inflammation, but the mutants fail to stimulate a regeneration response. To identify transcriptional changes that occur in zebrafish mutants undergoing progressive photoreceptor degeneration, RNA-seq transcriptional profiling was performed on cep290-/- and bbs2-/- retinas. The PANTHER Classification System was used to identify biological processes and signaling pathways that were differentially expressed between mutants and wild-type siblings during degeneration. As expected, genes associated with phototransduction were downregulated in cep290 and bbs2 mutants compared to wild-type siblings. Although both cep290 and bbs2 mutants undergo proliferation of rod precursors in response to retinal degeneration, the process of negatively regulating proliferation is enriched for upregulated genes, and this negative regulation may restrict proliferation of Müller glia and inhibit regeneration. A total of 815 differentially expressed genes (DEGs) were shared by cep290 and bbs2 retinas. Genes in pathways associated with inflammation, apoptosis, stress response, and PDGF signaling were overrepresented. Identifying the genes and biological pathways that are common in zebrafish models of inherited retinal degeneration provides a foundation for future studies on the mechanisms that regulate cell death as well as processes that prohibit Müller cell reprogramming or proliferation in a model capable of retinal regeneration. The pathways will provide targets for future interventions that may promote successful regeneration of lost photoreceptors.
Insights
Zebrafish mutants with inherited retinal degeneration show inflammation and cell death pathways, failing to regenerate photoreceptors. Shared genes in cep290 and bbs2 mutants highlight barriers to Müller glial cell reprogramming and regeneration.
Area of Science:
- * Ophthalmology and Regenerative Medicine
- * Molecular Biology and Genetics
- * Zebrafish as a model organism for retinal research
Background:
- * Adult zebrafish possess a remarkable capacity for retinal regeneration following injury, involving Müller glial cell activation.
- * Mutations in cep290 or bbs2 lead to progressive photoreceptor degeneration and inflammation, but lack a regenerative response.
- * Understanding the molecular basis for the failure of regeneration in these mutants is crucial for developing therapeutic strategies.
Purpose of the Study:
- * To identify transcriptional differences in zebrafish retinas with cep290 or bbs2 mutations during progressive photoreceptor degeneration.
- * To pinpoint shared biological processes and signaling pathways dysregulated in these models of inherited retinal degeneration.
- * To uncover molecular mechanisms that may inhibit Müller glial cell reprogramming and subsequent retinal regeneration.
Main Methods:
- * RNA-sequencing (RNA-seq) transcriptional profiling of cep290-/- and bbs2-/- zebrafish retinas compared to wild-type siblings.
- * Utilized the PANTHER Classification System for analyzing differentially expressed genes (DEGs) and associated biological pathways.
- * Focused on identifying shared DEGs and overrepresented pathways between the two mutant models.
Main Results:
- * Phototransduction genes were downregulated in both cep290 and bbs2 mutants.
- * Genes involved in the negative regulation of proliferation were upregulated, potentially inhibiting Müller glial cell proliferation.
- * A total of 815 DEGs were common to both mutants, enriched in pathways for inflammation, apoptosis, stress response, and PDGF signaling.
Conclusions:
- * Shared transcriptional pathways in cep290 and bbs2 mutants reveal molecular barriers to retinal regeneration.
- * Identifying these pathways provides targets for future interventions aimed at promoting photoreceptor regeneration.
- * This study lays the groundwork for understanding cell death regulation and Müller cell reprogramming inhibition in inherited retinal degeneration.
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