On the quantification of intracellular proteins in multifluorescence-labeled rat brain slices using slide-based cytometry.

In several brain regions, a subpopulation of neurons exists being characterized by the expression of a peculiar form of extracellular matrix, a so-called perineuronal net (PNN). We have previously shown that the PNN can bind large amounts of iron due to its polyanionic charge. Because free iron can generate reactive oxygen species thus being potentially toxic, the PNN may have a protective function by "scavenging" this free iron. Because of this ability, we have hypothesized that PNN-related neurons have an altered iron-specific metabolism. Thus, to compare the intracellular concentrations of iron containing proteins, specifically, the iron storage protein ferritin H between neurons with and without a PNN, we have used slide-based cytometry with image-based threshold-boundary cell detection on brain sections. In tissue sections, the integrity of the extracellular matrix, especially the characteristic PNNs, is preserved, which is necessary for the identification of the two neuronal subpopulations. A multilabeling approach was chosen to select neurons (neuronal marker NeuN), to classify the neurons according to their subtype (matrix marker Wisteria floribunda agglutinin), and to quantify the protein concentration (protein marker). Using this novel method, we were able to detect a relative difference in protein concentration as low as 12% between the two subpopulations of neurons in the neuronal population of the rat parietal cortex.