Personalized Proteomics for Precision Health: Identifying Biomarkers of Vitreoretinal Disease

Abstract

Proteomic analysis is an attractive and powerful tool for characterizing the molecular profiles of diseased tissues, such as the vitreous. The complexity of data available for analysis ranges from single (e.g., enzyme-linked immunosorbent assay [ELISA]) to thousands (e.g., mass spectrometry) of proteins, and unlike genomic analysis, which is limited to denoting risk, proteomic methods take snapshots of a diseased vitreous to evaluate ongoing molecular processes in real time. The proteome of diseased ocular tissues was recently characterized, uncovering numerous biomarkers for vitreoretinal diseases and identifying protein targets for approved drugs, allowing for drug repositioning. These biomarkers merit more attention regarding their therapeutic potential and prospective validation, as well as their value as reproducible, sensitive, and specific diagnostic markersTranslational RelevancePersonalized proteomics offers many advantages over alternative precision-health platforms for the diagnosis and treatment of vitreoretinal diseases, including identification of molecular constituents in the diseased tissue that can be targeted by available drugs.

Metabolite therapy guided by liquid biopsy proteomics delays retinal neurodegeneration

“…Neurodegenerative diseases, however, currently lack early detection methods for diagnosis and screening. In the case of retinal degenerative diseases, we have previously shown that liquid biopsies of the adjacent vitreous fluid can capture intracellular events in the neural retinal network that can guide diagnosis and treatment [28,47,61]. Advancements in this approach could allow for serial sampling and longitudinal monitoring of disease progress without the need to biopsy the neurosensory retina [27,29].…”

“…p<0.05). The decrease in retinal protein expression and corresponding increase in vitreous protein expression suggested that the degenerating neural retina may leak proteins into the vitreous, similar to that seen in human patient samples [28,47]. We then compared the list of proteins highly-abundant in control mouse retinas to that of the elevated proteins in Pde6ɑ D670G vitreous at the onset of neuronal cell death (P15).…”

Proteomic insight into the pathogenesis of CAPN5-vitreoretinopathy

“…Due to the rarity of surgical samples from CAPN5-NIV patients, we opted for an unbiased data-independent acquisition (DIA) approach which allows for the relative quantification of proteins in our samples. For more reliable and sensitive quantification of candidate biomarkers, a selective reaction monitoring (SRM) approach or multiplex ELISA would be more appropriate in future studies 11 .…”

“…Proteomic analysis is a powerful tool for studying the molecular basis of inflammatory diseases, like CAPN5-NIV 9 , 11 , 43 , 44 . Although several CAPN5-NIV-causing mutations have been identified, it is unclear how a hyperactive protease leads to retinal disease.…”

“…Since different proteomic platforms can give different results, we sought to obtain a more global view of the CAPN5-NIV vitreous proteome at each stage. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a powerful, unbiased analytical technique that ionizes molecular species in complex biochemical mixtures and sorts ions based on their mass-to-charge ratio ( m/z ) 10 , 11 . This technique is used in a “shotgun” approach to catalog and quantify the hundreds to thousands of proteins in a biological sample, which is often performed in tandem with liquid chromatography to separate peptides before they are ionized 10 .…”