Evolution of gene expression patterns in a model of branching morphogenesis

Branching morphogenesis of the ureteric bud in response to unknown signals from the metanephric mesenchyme gives rise to the urinary collecting system and, via inductive signals from the ureteric bud, to recruitment of nephro ns from undifferentiated mesenchyme. An established cell culture model for this process employs cells of ureteric bud origin (UB) cultured in extracel lular matrix and stimulated with conditioned media (BSN-CM) from a metaneph ric mesenchymal cell line (H. Sakurai, E. J. Barros, T. Tsukamoto, J. Baras ch, and S. K. Nigam. Proc. Natl. Acad. Sci. USA 94: 6279-6284, 1997.). In t he presence of BSN-Chl, the UB cells form branching tubular structures remi niscent of the branching ureteric bud. The pattern of gene regulation in th is model of branching morphogenesis of the kidney collecting system was inv estigated using high-density cDNA arrays. Software and analytical methods w ere developed for the quantification and clustering of genes. With the use of a computational method termed "vector analysis," genes were clustered ac cording to the direction and magnitude of differential expression in n-dime nsional log-space. Changes in gene expression in response to the BSN-CM con sisted primarily of differential expression of transcription factors with p reviously described roles in morphogenesis, downregulation of pro-apoptotic genes accompanied by upregulation of anti-apoptotic genes, and upregulatio n of a small group of secreted products including growth factors, cytokines , and extracellular proteinases. Changes in expression are discussed in the context of a general model for epithelial branching morphogenesis. In addi tion, the cDNA arrays were used to survey expression of epithelial markers and secreted factors in UB and BSN cells, confirming the largely epithelial character of the former and largely mesenchymal character of the later. Sp ecific morphologies (cellular processes, branching multicellular cords, etc .) were shown to correlate with the expression of different, but overlappin g, genomic subsets, suggesting differences in morphogenetic mechanisms at t hese various steps in the evolution of branching tubules.