Proteomics-Based Identification of Retinal Protein Networks Impacted by Elevated Intraocular Pressure in the Hypertonic Saline Injection Model of Experimental Glaucoma.

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To facilitate a better understanding of the underlying molecular processes and mechanisms, we report a study focusing on alterations of the retina proteome by induced ocular hypertension in a rat model of the disease. Glaucomatous processes were modeled through sclerosing the aqueous outflow routes of the eyes by hypertonic saline injections into an episcleral vein. Mass spectrometry-based quantitative retina proteomics using a label-free shotgun methodology identified over 200 proteins significantly affected by ocular hypertension. Various facets of glaucomatous pathophysiology were revealed through the organization of the findings into protein interaction networks and by pathway analyses. Concentrating on retinal neurodegeneration as a characteristic process of the disease, elevated intraocular pressure-induced alterations in the expression of selected proteins were verified by targeted proteomics based on nanoflow liquid chromatography coupled with nano-electrospray ionization tandem mass spectrometry using the parallel reaction monitoring method of data acquisition. Acquired raw data are shared through deposition to the ProteomeXchange Consortium (PXD042729), making a retina proteomics dataset on the selected animal model of glaucoma available for the first time.", "claims": [{"id": "claim-method", "statement": "Our LFQ applied spectral counting and Fisher’s exact tests [32] with corrections for multiple testing [33] to obtain proteins with statistically significant differences in their expression in the OHT versus normotensive retinae (Table S3).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37628770", "locator": "sections[2] \"2. Results\" paragraph 2", "quote": "Our LFQ applied spectral counting and Fisher’s exact tests [32] with corrections for multiple testing [33] to obtain proteins with statistically significant differences in their expression in the OHT versus normotensive retinae (Table S3)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [31] partner repository with the dataset identifier PXD042729 and 10.6019/PXD042729.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37628770", "locator": "sections[16] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [31] partner repository with the dataset identifier PXD042729 and 10.6019/PXD042729."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Elevated intraocular pressure affected 204 retina proteins, comprising 92 downregulated and 112 upregulated proteins.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37628770", "locator": "sections[2] \"2. Results\" paragraph 2", "quote": "Altogether, the elevated IOP affected 204 retina proteins when we filtered the list of these proteins with thresholds of ≤0.5 (downregulation) and ≥2.0 (upregulation) in spectral count ratios."}, {"asset": "source:pmid:37628770", "locator": "sections[2] \"2. 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