Microarray analysis of GFP-expressing mouse Dopamine neurons isolated by laser capture microdissection

The Central Nervous System (CNS) contains an enormous variety of cell types which organize in complex networks. The lack of adequate markers to discern unequivocally among this cellular heterogeneity make the task of dissecting out such neural networks and the cells that comprise them very challenging. The present study represents a “bottom-up” approach that entails a description of A9 and A10 nuclei, which are components of the mesencephalic dopaminergic system, and the identification of their molecular make-up through microarray analysis of their gene expression profiles. These mesencephalic dopaminergic nuclei give rise to the mesocortical and mesostriatal projections and are well known for their roles in initiation of movement, reward behaviour and neurobiology of addiction. Moreover, in post mortem brains of Parkinson Disease patients a specific topographic pattern of degeneration of these neurons, also recapitulated in experimental animal models, is noted, with A9 neurons presenting with a higher vulnerability to degeneration with respect to A10 cells among which, neuron loss is almost negligible. Molecular differences may be at the basis of this different susceptibility. In this study we have optimized a protocol for laser-assisted microdissection of fluorescent-expressing cells and have taken advantage of a line of transgenic mice TH-GFP/21-31, which express GFP under the TH promoter in all CA cells, to guide laser capture microdissection of A9 and A10 mDA neurons for differential informative cDNA microarray profiling. Results show that our optimized method retains the GFP-fluorescence of DA cells and achieves good tissue morphology visualization. Moreover, RNA of high quality and good reproducibility of hybridizations support the validity of the protocol. Many of the genes that resulted differentially expressed from this analysis were found to be genes previously known to specifically define the different identities of the two DA neuronal nuclei. Transcripts were verified for expression, in DA neurons, using the collection of in situ hybridization in the Allen Brain Atlas. We have identified 592 differentially expressed transcripts (less than 8%) of which 242 showing higher expression in A9 and 350 showing higher expression in A10. Categorical analysis showed that transcripts associated with mitochondria and energy production were enriched in A9, while transcripts involved in redox homeostasis and stress response resulted enriched in A10. Of all the differentially expressed genes, eight transcripts (Mif, Hnt, Ndufa10, Aurka, Cs, enriched in A9 neurons and Pdia5, Whrn, and Gpx3 enriched in A10 neurons), verified with the Allen Brain Atlas and not noted or confirmed as differentially expressed before, emerged from this analysis. These and other selected genes are discussed.