A catalogue of gene expression in the developing kidney

Background. Although many genes with important function in kidney morphogenesis have been described, it is clear that many more remain to be discovered. Microarrays allow a more global analysis of the genetic basis of kidney organogenesis. Methods. In this study, Affymetrix U74Av2 microarrays, with over 12,000 genes represented, were used in conjunction with robust target microamplification techniques to define the gene expression profiles of the developing mouse kidney. Results. Microdissected murine ureteric bud and metanephric mesenchyme as well as total kidneys at embryonic day E11.5, E12.5, E13.5, E16.5, and adult were examined. This work identified, for example, 3847 genes expressed in the E12.5 kidney. Stringent comparison of the E12.5 versus adult recognized 428 genes with significantly elevated expression in the embryonic kidney. These genes fell into several functional categories, including transcription factor, growth factor, signal transduction, cell cycle, and others. In contrast, surprisingly few differences were found in the gene expression profiles of the ureteric bud and metanephric mesenchyme, with many of the differences clearly associated with the more epithelial character of the bud. In situ hybridizations were used to confirm and extend microarray-predicted expression patterns in the developing kidney. For three genes, Cdrap, Tgfbi, and Col15a1, we observed strikingly similar expression in the developing kidneys and lungs, which both undergo branching morphogenesis. Conclusion. The results provide a gene discovery function, identifying large numbers of genes not previously associated with kidney development. This study extends developing kidney microarray analysis to the powerful genetic system of the mouse and establishes a baseline for future examination of the many available mutants. This work creates a catalogue of the gene expression states of the developing mouse kidney and its microdissected subcomponents.