Effects of post-mortem intervals on regional brain protein profiles in rats using SELDI-TOF-MS analysis

Identification of disease-associated proteins is critical for elucidating CNS disease mechanisms and elaborating novel treatment strategies. It requires post-mortem tissue analysis which can be significantly affected by the collection process, post-mortem intervals (PMIs), and storage conditions. To assess the effect of time and storage conditions on brain protein stability, SELDI-TOF-MS protein profiles were assessed in rat frontal cortex, caudate-putamen, hippocampus and medulla samples collected after various PMIs (0, 6, 12, 24, 48, and 72 h) at 4 °C or at room temperature (RT) storage. Regions of interest were isolated from cryosections (tissue apposition, TA), or micropunched from cryosections apposed on filter paper (paper apposition, PA), and applied onto an NP20 ProteinChip array. Protein alterations, while greater at RT than at 4 °C, were detected at 6h then differentially evolved in the various brain regions, with greater alterations in the caudate-putamen (60%) and the cortex (48%). Overall, our sensitive analytical method allowed unveiling of different patterns of protein susceptibility to PMI and to storage temperature in the various brain regions. Some protein peaks were altered in all brain regions and may potentially serve as markers of the PMI status of the brain, or for reference values when studying new proteins. Changes in disease-related proteins within post-mortem samples can be greatly affected by PMI and storage conditions, particularly when studying fragile and/or low abundant protein/peptides in tissues sampled from the caudate-putamen and neocortex.