The use of representational difference analysis and cDNA microarrays in neural repair research

Genetic subtraction studies may be useful tools for neural repair research by identifying genes expressed under one condition, but not under another. However, these studies suffer from some limitations, including a lack of heterogeneity of subtracted cDNA pools and the difficulty of screening out false positives in the subtracted pools. Our strategy to overcome these difficulties was to combine one subtractive method representational difference analysis - with screening of the subtracted products using a custom cDNA microarray. Using the neurosphere culture system, we have used this stepwise approach in order to identify genes that are selectiveley expressed by CNS progenitor cells, but not by more differentiated cells. Following microarray screening, we confirmed the localization of putatively differentially expressed clones by in situ hybridization analysis. These genes, both novel and previously identified, now become candidate therapeutic targets for CNS repair strategies.