Proteomic and Phosphoproteomic Characteristics of the Retina, Choroid, and Sclera in Guinea Pigs with Form-Deprivation Myopia

Myopia is a growing global public health concern. Recent studies have revealed that the regulation of eye growth occurs via a complex signaling cascade, which originates in the retina and across the choroid to the sclera. Identifying key proteins and specific biological processes (BPs) in the retina, choroid, and sclera is crucial for understanding the molecular mechanisms underlying myopia development. We conducted comprehensive proteomic and phosphoproteomic analyses of the retina, choroid, and sclera from form-deprivation myopia guinea pigs using liquid chromatography-tandem mass spectrometry. Differentially expressed proteins and phosphosites were identified, followed by functional annotation and signaling pathway enrichment analyses. The expression of key proteins was assessed using Western blotting and enzyme-linked immunosorbent assay. Distinct proteomic and phosphoproteomic profiles were observed across the three tissues, with 6470, 6708, and 3236 proteins and 9613, 9416, and 3685 phosphosites in the retina, choroid, and sclera, respectively. Proteomic analysis showed that neural signal transduction was enriched in the retina, with downregulation of NTRK2, suggesting impaired neurotrophic signaling. The upregulation of SYK and BTK, along with increased NF-κB, p65, and IL-1β levels in the choroid, indicated enhanced inflammatory responses. TNNT3, TPM2, and ACTN3 were upregulated in the sclera, reflecting cytoskeletal remodeling associated with scleral expansion. Phosphoproteomic analysis indicated key roles of phosphoproteins in BPs, particularly the spliceosome signaling pathway, which was broadly involved across all three tissues. Kinase network analysis revealed PRPF4B as a key kinase for SF3B1, suggesting the potential regulation roles of RNA splicing in myopia progression. The present study systematically elucidates the proteomic and phosphoproteomic characteristics of the retina, choroid, and sclera of form-deprivation myopia in guinea pigs, highlighting significant tissue-specific BPs to myopia. The findings provide a theoretical foundation for understanding that different tissues exhibit distinct biological reactions to myopia, each through specific signaling pathways and regulatory mechanisms.