Changes in gene expression patterns in the ureteric bud and metanephric mesenchyme in models of kidney development.

BACKGROUND In a recent study, the pattern of gene expression during development of the rat kidney was analyzed using high-density DNA array technology (Stuart RO, Bush KT, Nigam SK, Proc Natl Acad Sci USA 98:5649-5654, 2001). This approach, while shedding light on global patterns of gene expression in the developing kidney, does not provide insight into the contributions of genes that might be part of the morphogenetic program of the ureteric bud (UB) and metanephric mesenchyme (MM), the two tissues that interact closely during nephron formation. METHODS We have now used high-density DNA arrays together with a double in vitro transcription (dIVT) approach to examine gene expression patterns in in vitro models for morphogenesis of the rat UB (isolated UB culture) and MM (coculture with embryonic spinal cord) and compared this data with patterns of gene expression in the whole embryonic kidney at different stages of development. RESULTS The results indicate that different sets of genes are expressed in the UB and MM as morphogenesis occurs. The dIVT data from the in vitro UB and MM culture models was clustered hierarchically with single IVT data from the whole embryonic kidney obtained at different stages of development, and the global patterns of gene expression were remarkably compatible, supporting the validity of the approach. The potential roles of genes whose expression was associated with the individual tissues were examined, and several pathways were identified that could have roles in kidney development. For example, hepatocyte nuclear factor-6 (HNF-6), a transcription factor potentially upstream in a pathway leading to the expression of KSP-cadherin was highly expressed in the UB. Embigin, a cell adhesion molecule important in cell/extracellular matrix (ECM) interactions, was also found in the UB and may serve as a Dolichos biflorus binding protein in the kidney. ADAM10, a disintegrin-metalloprotease involved in Delta-Notch signaling and perhaps Slit-Robo signaling, was also highly expressed in late UB. Celsr-3, a protein, which along with members of the Wnt-frizzled transduction cascade, might be involved in the polarization of the forming nephron, was found to be highly expressed in differentiating MM. DDR2, a member of the discoidin domain receptor family, which is thought to function in the activation of matrix metalloproteinase-2 (MMP-2), was also found to be highly expressed in differentiating MM. It is also interesting to note that almost 10% of the highly expressed genes in both tissues were associated with neuronal growth and/or differentiation. CONCLUSION The data presented in this study point to the power of combining in vitro models of kidney development with high-density DNA arrays to identify the genes involved in the morphogenetic process. Clear differences were found between patterns of genes expressed by the UB and MM at different stages of morphogenesis, and many of these were associated with neuronal growth and/or differentiation. Together, the high-density microarray data not only begin to suggest how separate genetic programs in the UB and MM orchestrate the formation of the whole kidney, but also suggest the involvement of heretofore largely unexplored developmental pathways (involving HNF-6, ADAM-10, Celsr-3, DDR2, and other genes) in nephrogenesis.