Newrzella D, Pahlavan PS, Krüger C, Boehm C, Sorgenfrei O, Schröck H, Eisenhardt G, Bischoff N, Vogt G, Wafzig O, Rossner M, Maurer MH, Hiemisch H, Bach A, Kuschinsky W, Schneider A. The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia. BMC Genomics. 2007;8:370. PubMed.
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Banner Research Institute
The combination of laser capture microdissection of defined cell classes with array hybridization represents a significant advance, and this study demonstrates this by revealing differences between CA1 and CA3 cell populations at baseline and in response to ischemia. The abstract does not specify how sufficient transcript for array hybridization was obtained. The presumption is that this was achieved by combining RNA from many cells or by amplification of RNA from fewer cells. In collaboration with Yan Cao of Affymetrix, we have determined that 100 cells with amplification is an approximate minimum for adequate material for AFFY arrays.
Therein lies the drawback when multiple cells are required. In the case of the present study one may presume variability in the responses of individual cells to ischemia, just as there is variability in the presence of NFT in neurons from AD brain. Thus, the picture that emerges represents an average of cells that respond dramatically to, e.g. ischemia, and cells that respond little if at all. One solution to this averaging effect is to find a way to select cells that are more equivalent by, for example, prior immunhistochemistry. The usual IHC procedures will wash out significant amounts of RNA, but it is possible to develop procedures that are kinder to the RNA population.
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