Retinal Proteins During Postnatal Development in Mice Can Be Classified Into Four Major Types Based on Their Proteomic Trajectories

Abstract

Abstract: : Purpose: As a first step toward the understanding of retinal physiology and pathology in proteomic terms, we attempt to classify the retinal proteins displayed on two–dimensional (2–D) gels based on their time–dependent expression patterns, which we designate "proteomic trajectory", along the postnatal developmental axis. Methods: Retinas of C57/B6 mice were collected at postnatal (P) days 1, 3, 5, 7, 9, 14, 21 and at the adult stage (P>28). After separating the proteins by 2–D gel electrophoresis, the gels were stained with Coomassie blue, scanned, and analyzed by Progenesis Workstation (Nonlinear Dynamics). Each protein spot was quantified and normalized to the total density of the gel and the proteomic trajectory along the developmental axis was obtained. The results were averaged from four independent experiments. The proteomic trajectories were clustered by self–organizing mapping (SOM) using GeneCluster2. For protein identification each spot was excised and subjected to in–gel digestion by trypsin, followed by peptide mass fingerprinting (PMF) by Voyager Elite (Applied Biosystems) matrix–assisted laser desorption/ionization time–of–flight mass spectrometer (MALDI–TOF MS) and by Axima QIT (Shimadzu/Kratos) MALDI–quadrupole ion trap TOF MS. PMF search and confirmation were performed by Protein Prospector and MASCOT. Results: Among 523 protein spots analyzed, we identified ca 400 proteins. These proteins can be clustered by SOM into four major types, each exhibiting characteristic proteomic trajectory: Juvenile–type (J–Type), showing abundant expression in the early postnatal stages and declining along the maturation process; Transient–type (T–Type), showing transient expression during the development; Adult–type (A–Type), showing increased expression in the later stages of development toward maturation; and Constitutive–Type (C–Type), being expressed relatively constant during the entire developmental stages. We also observed that proteins belonging to each group could further be classified into subtypes by refining the profiles of the proteomic trajectories. Conclusions: The proteins in the developing mouse retina can be classified into four major groups based on their proteomic trajectories. The roles of the proteins in each group will be interpreted.

Keywords: proteomics • retinal development • retina