Proteome profiling of vitreoretinal diseases by cluster analysis

• Published in: Proteomics. Clinical applications Vol. 2; no. 9; pp. 1265 - 1280
• Main Authors: Shitama, Tomomi, Hayashi, Hideyuki, Noge, Sumiyo, Uchio, Eiichi, Oshima, Kenji, Haniu, Hisao, Takemori, Nobuaki, Komori, Naoka, Matsumoto, Hiroyuki
• Format: Journal Article
• Language: English
• Published: Weinheim WILEY-VCH Verlag 01.09.2008; WILEY‐VCH Verlag; Wiley
• Subjects: Biological and medical sciences; Cluster analysis; Diverse techniques; Fundamental and applied biological sciences. Psychology; Marker proteins; Medical sciences; Molecular and cellular biology; Ophthalmology; Quantitative proteomics; Retinopathies; Two-dimensional gel; Vitreoretinal diseases; Cluster analysis; Eye disease; Marker proteins; Two-dimensional gel; Vitreous phase; Retinopathy; Quantitative proteomics; Subretinal fluid; Proteomics; Proteome; Vitreoretinal diseases; Protein
• ISSN: 1862-8346; 1862-8354
• DOI: 10.1002/prca.200800017

Vitreous samples collected in retinopathic surgeries have diverse properties, making proteomics analysis difficult. We report a cluster analysis to evade this difficulty. Vitreous and subretinal fluid samples were collected from 60 patients during surgical operation of non‐proliferative diabetic retinopathy, proliferative diabetic retinopathy, proliferative vitreoretinopathy, and rhegmatogenous retinal detachment. For controls, we collected vitreous fluid from patients of idiopathic macular hole, epiretinal, and from a healthy postmortem donor. Proteins from these samples were subjected to quantitative proteomics using two‐dimensional gel electrophoresis. We selected 105 proteins robustly expressed among ca. 400 protein spots and subjected them to permutation test. By using permutation test analysis we observed unique variations in the expression of some of these proteins in vitreoretinal diseases when compared to the control and to each other: (i) the levels of inflammation‐associated proteins such as alpha1‐antitrypsin, apolipoprotein A4, albumin, and transferrin were significantly higher in all four types of vitreoretinal diseases, and (ii) each vitreoretinal disease elevated a unique set of proteins, which can be interpreted based on the pathology of retinopathy. Our protocol will be effective for the study of protein expression in other types of clinical samples of diverse properties.