Different protein profiles in inferior colliculus and cerebellum: a comparative proteomic study

The characteristic features of individual brain regions are determined by anatomical, physiological, and biochemical properties, which are caused by the nature and amount of proteins expressed. Proteomics is a powerful technology for assessing different protein profiles, comparing hundreds of proteins simultaneously. Here we performed a semi-quantitative proteomic analysis of two prominent brain regions in the male adult rat, the inferior colliculus and the cerebellum. Both play important roles in sensorimotor integration but have distinct anatomical and biochemical features. Soluble proteins of mainly cytoplasmic origin were obtained through subcellular fractionation, separated by two-dimensional gel electrophoresis, and identified by matrix-assisted laser desorption/ionization mass spectrometry. Out of 169 annotated and quantified spots, 40 (24%) displayed significant differences in intensity between the two brain regions. Of those, 21 spots (containing 26 proteins) were more intense in the inferior colliculus and 19 spots (containing 25 proteins) in the cerebellum. The inferior colliculus displayed a higher abundance of proteins involved in vesicular trafficking, such as dynamin-1 and cofilin-1. In the cerebellum, Ca2+ -binding proteins (calbindin and calretinin) as well as 14-3-3 proteins were more abundant. Both protein groups play a central role in cellular signaling. Finally, several differences occurred among proteins involved in cellular energy metabolism. Our study presents a proof of principle to demonstrate marked heterogeneity of proteins between two brain samples. The heterogeneity is likely associated with functional differences, warranting further histological and physiological analyses.