Modulation of intestinal gene expression by dietary zinc status: Effectiveness of cDNA arrays for expression profiling of a single nutrient deficiency

Mammalian nutritional status affects the homeostatic balance of multiple ph ysiological processes and their associated gene expression. Although DNA ar ray analysis can monitor large numbers of genes, there are no reports of ex pression profiling of a micronutrient deficiency in an intact animal system . in this report, we have tested the feasibility of using cDNA arrays to co mpare the global changes in expression of genes of known function that occu r in the early stages of rodent zinc deficiency. The gene-modulating effect s of this deficiency were demonstrated by real-time quantitative PCR measur ements of altered mRNA levels for metallothionein 1, zinc transporter 2, an d uroguarylin, all of which have been previously documented as zinc-regulat ed genes. As a result of the low level of inherent noise within this model system and application of a recently reported statistical tool for statisti cal analysis of microarrays [Tusher, V.G., Tibshirani, R. & Chu, G. (2001) Proc. Natl. Acad. Sci. USA 98, 5116-5121], we demonstrate the ability to re producibly identify the modest changes in mRNA abundance produced by this s ingle micronutrient deficiency. Among the genes identified by this array pr ofile are intestinal genes that influence signaling pathways, growth, trans cription, redox, and energy utilization. Additionally, the Influence of die tary zinc supply on the expression of some of these genes was confirmed by real-time quantitative PCR. Overall, these data support the effectiveness o f cDNA array expression profiling to investigate the pleiotropic effects of specific nutrients and may provide an approach to establishing markers for assessment of nutritional status.