Research Article: Proteomic analysis of the human retina reveals region-specific susceptibilities to metabolic- and oxidative stress-related diseases

Date Published: February 21, 2018

Publisher: Public Library of Science

Author(s): Gabriel Velez, Daniel A. Machlab, Peter H. Tang, Yang Sun, Stephen H. Tsang, Alexander G. Bassuk, Vinit B. Mahajan, Alfred S Lewin.


Differences in regional protein expression within the human retina may explain molecular predisposition of specific regions to ophthalmic diseases like age-related macular degeneration, cystoid macular edema, retinitis pigmentosa, and diabetic retinopathy. To quantify protein levels in the human retina and identify patterns of differentially-expressed proteins, we collected foveomacular, juxta-macular, and peripheral retina punch biopsies from healthy donor eyes and analyzed protein content by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein expression was analyzed with 1-way ANOVA, gene ontology, pathway representation, and network analysis. We identified a mean of 1,974 proteins in the foveomacular retina, 1,999 in the juxta-macular retina, and 1,779 in the peripheral retina. Six hundred ninety-seven differentially-expressed proteins included those unique to and abundant in each anatomic region. Proteins with higher expression in each region include: heat-shock protein 90-alpha (HSP90AA1), and pyruvate kinase (PKM) in the foveomacular retina; vimentin (VIM) and fructose-bisphosphate aldolase C (ALDOC); and guanine nucleotide-binding protein subunit beta-1 (GNB1) and guanine nucleotide-binding protein subunit alpha-1 (GNAT1) in the peripheral retina. Pathway analysis identified downstream mediators of the integrin signaling pathway to be highly represented in the foveomacular region (P = 6.48 e–06). Metabolic pathways were differentially expressed among all retinal regions. Gene ontology analysis showed that proteins related to antioxidant activity were higher in the juxta-macular and the peripheral retina, but present in lower amounts in the foveomacular retina. Our proteomic analysis suggests that certain retinal regions are susceptible to different forms of metabolic and oxidative stress. The findings give mechanistic insight into retina function, reveal important molecular processes, and prioritize new pathways for therapeutic targeting.

Partial Text

The human retina can be divided into three regions: fovea, macula, and periphery (Fig 1A). They are unique in functionality and susceptibility to diseases such as age-related macular degeneration (AMD), retinitis pigmentosa (RP), proliferative diabetic retinopathy (PDR), and cystoid macular edema (CME). To develop targeted therapies, it is important to understand the molecular basis of their pathophysiology.

The human retina is composed of distinct regions that are each susceptible to diseases such as AMD, PDR, RP, and CME (S6 Fig). Proteomic analysis using mass spectrometry is an unbiased method for analyzing global and regional protein expression. Our data demonstrates significant molecular differences between retinal regions that may provide insight into the underlying mechanisms for various diseases. The identified differences in regional protein expression between the retina and RPE-choroid is not surprising as they carry out distinct physiological roles (S4 Fig) [13]. We anticipate that further comparison between these proteomic profiles may elucidate new differences between the molecular functions and pathological susceptibilities of these two tissues.

Proteomic analysis is a powerful tool for studying retinal molecular functions. Unlike gene expression, proteomic analysis can identify dynamic changes in regional protein expression in both healthy and diseased tissue.[6–8] Our dataset points to differential expression of antioxidant and metabolic proteins in the three retinal regions, a finding that has implications for diseases that manifest in unique patterns or localize to specific regions, suggesting that prophylactic targeting of ROS and metabolic reprogramming is essential to treat a variety of retinal diseases. Further interrogation of our dataset should generate additional hypotheses for future validation studies and provide an exciting opportunity to treat the most devastating blinding diseases.




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