Hyperlipidemia is a chronic disease characterized by elevated blood cholesterol and triglycerides and there is accumulated evidence that the disease might affect brain functions. Here we report on a proteomic analysis of the brain proteins in hyperlipidemic mice. Hyperlipidemia was successfully induced in mice by a 20 week high-fat diet (HFD) feeding (model group). A control group with a normal diet and a treatment group with HFD-fed mice treated with a lipid-lowering drug simvastatin (SIM) were established accordingly. The proteins were extracted from the left and right cerebrum hemispheres of the mice in the three groups and subjected to shotgun proteomic analysis. A total of 4,422 proteins were detected in at least half of the samples, among which 324 proteins showed significant difference (fold change >1.5 or <0.67, p < 0.05) in at least one of the four types of comparisons (left cerebrum hemispheres of the model group versus the control group, right cerebrums of model versus control, left cerebrums of SIM versus model, right cerebrums of SIM versus model). Biological process analysis revealed many of these proteins were enriched in the processes correlated with lipid metabolism, neurological disorders, synaptic events and nervous system development. For the first time, it has been reported that some of the proteins have been altered in the brain under the conditions of HFD feeding, obesity or hyperlipidemia. Further, 22 brain processes-related proteins showed different expression in the two cerebrum hemispheres, suggesting changes of the brain proteins caused by hyperlipidemia might also be asymmetric. We hope this work will provide useful information to understand the effects of HFD and hyperlipidemia on brain proteins.
SDS-PAGE has often been used in proteomic analysis, but generally for sample prefractionation although the technique separates proteins by molecular masses (M w s) and the information would contribute to proteoform-level analysis. Here, we report a method that combines SDS-PAGE, whole-gel slicing, and quantitative LC− MS/MS for establishing gel distributions of several thousand proteins in a proteome. A previously obtained data set on rat cerebral cortex with cerebral ischemia-reperfusion injury 1 was analyzed, and the gel distributions of 5906 proteins were reconstructed. These distributions, referred to as 1DE-MS profiles, revealed that about 30% of the proteins had more than one proteoform detected in the gels. The profiles were categorized into six types by distribution (narrow, dispersed, or broad) and relative deviations between the abundance-peak apparent M w s and calculated M w s. Only 56% of the proteins showed narrow distributions and matched M w s, while the others had rather complex profiles. Bioinformatic analysis on example profiles showed the resolved proteoforms involved alternative splicing, proteolytic processing, glycosylation and ubiquitination, fragmentation, and probably transmembrane structures. Profile-based differential analysis revealed that many of the disease-caused changes were proteoform dependent. This work provided a proteome-scale view of protein distributions in SDS-PAGE gels, and the method would be useful to obtain proteoform-correlated information for in-depth proteomics.
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