The human eye proteome project

The Human Eye Proteome Project: Updates on an Emerging Proteome

The human eye is a complex organ consisting of multiple compartments with unique and specialized properties that reflect their varied functions. Although there have been advancements in ocular imaging and therapeutics over the past decade, the pathogenesis of many common eye diseases remains poorly understood. Proteomics is an invaluable tool to gain insight into pathogenesis, diagnosis, and treatment of eye diseases. By 2013, when the Human Eye Proteome Project (also known as the EyeOme) was founded, there were 4842 nonredundant proteins identified in the human eye. Twenty-three recent papers on the human eye proteome were identified in PubMed searches. These papers were used to compile an updated resource of 9782 nonredundant proteins in the human eye. This updated catalogue sheds light on the molecular makeup of previously undescribed proteomes within the human eye, including optic nerve, sclera, iris, and ciliary body, while adding additional proteins to previously characterized proteomes such as aqueous humor, lens, vitreous, retina, and retinal pigment epithelium/choroid. Although considerable advances have been made to characterize the complete proteome of the human eye, additional high-quality data are needed to confirm and quantify previously discovered eye proteins in both health and disease.

Proteomic analysis of corneal endothelial cell-descemet membrane tissues reveals influence of insulin dependence and disease severity in type 2 diabetes mellitus

The objective of this study was to characterize the proteome of the corneal endothelial cell layer and its basement membrane (Descemet membrane) in humans with various severities of type II diabetes mellitus compared to controls, and identify differentially expressed proteins across a range of diabetic disease severities that may influence corneal endothelial cell health. Endothelium-Descemet membrane complex tissues were peeled from transplant suitable donor corneas. Protein fractions were isolated from each sample and subjected to multidimensional liquid chromatography and tandem mass spectrometry. Peptide spectra were matched to the human proteome, assigned gene ontology, and grouped into protein signaling pathways unique to each of the disease states. We identified an average of 12,472 unique proteins in each of the endothelium-Descemet membrane complex tissue samples. There were 2,409 differentially expressed protein isoforms that included previously known risk factors for type II diabetes mellitus related to metabolic processes, oxidative stress, and inflammation. Gene ontology analysis demonstrated that diabetes progression has many protein footprints related to metabolic processes, binding, and catalysis. The most represented pathways involved in diabetes progression included mitochondrial dysfunction, cell-cell junction structure, and protein synthesis regulation. This proteomic dataset identifies novel corneal endothelial cell and Descemet membrane protein expression in various stages of diabetic disease. These findings give insight into the mechanisms involved in diabetes progression relevant to the corneal endothelium and its basement membrane, prioritize new pathways for therapeutic targeting, and provide insight into potential biomarkers for determining the health of this tissue.

Identification of proteins in the aqueous humor associated with cataract development using iTRAQ methodology

Proteins in the aqueous humor (AH) are important in the induction of cataract development. The identification of cataract-associated proteins assists in identifying patients and predisposed to the condition and improve treatment efficacy. Proteomics analysis has previously been used for identifying protein markers associated with eye diseases; however, few studies have examined the proteomic alterations in cataract development due to high myopia, glaucoma and diabetes. The present study, using the isobaric tagging for relative and absolute protein quantification methodology, aimed to examine cataract-associated proteins in the AH from patients with high myopia, glaucoma or diabetes, and controls. The results revealed that 445 proteins were identified in the AH groups, compared with the control groups, and 146, 264 and 130 proteins were differentially expressed in the three groups of patients, respectively. In addition, 44 of these proteins were determined to be cataract‑associated, and the alterations of five randomly selected proteins were confirmed using enzyme-linked immunosorbent assays. The biological functions of these 44 cataract-associated proteins were analyzed using Gen Ontology/pathways annotation, in addition to protein‑protein interaction network analysis. The results aimed to expand current knowledge of the pathophysiologic characteristics of cataract development and provided a panel of candidates for biomarkers of the disease, which may assist in further diagnosis and the monitoring of cataract development.

The proteomes of the human eye, a highly compartmentalized organ

Proteomics has now published a series of Dataset Briefs on the EyeOme from the HUPO Human Proteome Project with high-quality analyses of the proteomes of these compartments of the human eye: retina, iris, ciliary body, retinal pigment epithelium/choroid, retrobulbar optic nerve, and sclera, with 3436, 2929, 2867, 2755, 2711, and 1945 proteins, respectively. These proteomics resources represent a useful starting point for a broad range of research aimed at developing preventive and therapeutic interventions for the various causes of blindness.

Highlights of B/D-HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics: September 14-18, 2013, Yokohama, Japan

At the 12th Annual HUPO World Congress of Proteomics in Japan, the Human Proteome Project (HPP) presented 16 scientific workshop sessions. Here we summarize highlights of ten workshops from the Biology and Disease-driven HPP (B/D-HPP) teams and three from the HPP Resource Pillars. Highlights of the three Chromosome-centric HPP sessions appeared in the many articles of the 2014 C-HPP special issue of the Journal of Proteome Research .