Characterization of gene expression profiles of normal canineretina and brain using a retinal cDNA microarray

[摘要] Purpose: Construction of a canine retinal custom cDNA microarray forcomprehensive retinal gene expression profiling and application for theidentification of genes that are preferentially expressed in the retinaand brain lobes using a brain pool reference tissue.Methods: A cDNA microarray was constructed utilizing clones obtainedfrom a normalized canine retinal expressed sequence tag library. Geneexpression profiles were analyzed for normal retina, as well as thecortex of the frontal, occipital, and temporal brain regions. Eachsample was studied against a reference sample of pooled brain RNA. Datafrom a quantified scanned image were normalized using the loess subgridprocedure. Retina-enriched genes were identified using the SignificanceAnalysis of Microarrays (SAM) algorithm, and confirmed by northern blotanalyses for selected genes. Differences between biological samples weredisplayed using principal component analysis (PCA).Results: Expression profiles for each tissue set were analyzedagainst the common reference of pooled brain. Changes in expressionbetween the sample and the reference were higher in the retina (27.9%)than the individual brain tissues (2-6.6%). Furthermore, all individualretinal samples were clearly separated from any of the hybridizationsusing brain tissue in the PCA. The accuracy of observed changes inexpression has been confirmed by northern blot analysis using fiverandomly chosen genes that represented a wide range of differentexpression levels between retina and brain.Conclusions: We have established an accurate and robust microarraysystem suitable for the investigation of expression patterns in theretina and brain. Characterization of the gene expression profiles innormal retina will facilitate the understanding of the processes thatunderline differences between normal and diseased retinas.

[学科分类] 生物化学/生物物理