Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery

Background Sex as a biological variable is not a common consideration in molecular mechanistic or preclinical studies of retinal diseases. Understanding the sexual dimorphism of adult RPE and retina under physiological conditions is an important first step in improving our understanding of sex-based physio-pathological mechanisms. Methods Isobaric tags for relative and absolute quantitation (iTRAQ) were used for quantitative proteomics of male and female mouse retina and RPE (10 mice of each sex for each tissue type). Differentially expressed proteins were subjected to Gene Ontology (GO) analysis and Ingenuity Pathway Analysis (IPA). Results Differential expression analysis identified 38 differentially expressed proteins in the retina and 82 differentially expressed proteins in the RPE. Ingenuity pathway analysis identified the top canonical pathways differentially activated in the retina to be calcium transport I, nucleotide excision repair, fatty acid-b oxidation I and asparagine biosynthesis. In the RPE, the top canonical pathways were calcium signaling, dilated cardiomyopathy signaling, actin cytoskeletal signaling and RHOGDI signaling. Conclusions These results provide insights into sex differences in the retina and RPE proteome of mice and begin to shed clues into the sexual dimorphism seen in retinal diseases.

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Identifying Pathological Myopia Associated Genes with A Random Walk-Based Method in Protein-Protein Interaction Network

Zhang,

Huang,

Sun

et al. 2024

CBIO

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Background:: Pathological myopia, a severe variant of myopia, extends beyond the typical refractive error associated with nearsightedness. While the condition has a strong genetic component, the intricate mechanisms of inheritance remain elusive. Some genes have been associated with the development of pathological myopia, but their exact roles are not fully understood. Objective:: This study aimed to identify novel genes associated with pathological myopia Methods:: Our study leveraged DisGeNET to identify 184 genes linked with high myopia and 39 genes related to degenerative myopia. To uncover additional pathological myopia-associated genes, we employed the random walk with restart algorithm to investigate the protein-protein interactions network. We used the previously identified 184 high myopia and 39 degenerative myopia genes as seed nodes. Results:: Through subsequent screening tests, we discarded genes with weak associations, yielding 103 new genes for high myopia and 33 for degenerative myopia. Conclusion:: We confirmed the association of certain genes, including six genes that were confirmed to be associated with both high and degenerative myopia. The newly discovered genes are helpful to uncover and understand the pathogenesis of myopia.

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Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery

Cited by 5 publications

References 114 publications

Editorial for the Neurogenetics and Neurogenomics special issue

Editorial for the Neurogenetics and Neurogenomics special issue

Quantitative Proteomic Profiling Reveals Sexual Dimorphism in the Retina and RPE of C57BL6 mice.

Identifying Pathological Myopia Associated Genes with A Random Walk-Based Method in Protein-Protein Interaction Network

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