Systems analysis reveals interdependency of PKA and Wnt signaling during nephron development

Kidney development involves complex morphogenetic interactions, some of which are not currently well defined. The morphologic development of the nephron, in specific, is a well described process that is part of a robust literature on renal developmental morphogenesis. It is an aim of the field to elucidate mechanisms controlling the morphogenesis of the developing kidney. To achieve an understanding of renal morphogenetic programs a wealth of microarray data has been collected describing temporal and spatial aspects of the developing kidney in vivo. This data is augmented with microarray data from in vitro systems that recapitulate aspects of renal development. This data has largely been examined in isolation, and to begin addressing renal development from an integrative perspective we collect diverse spatial and temporal microarray data sets and together with the in vitro models begin an integrated analysis. The aim is to provide insight into morphogenetic programs controlling renal development and provide a model for analysis of any complex process for which disparate data exists. The “crossing” of in vivo developmental data by multiple methods provides contextualization to the data sets. Integration of in vivo spatial data with in vitro model microarray data highlighted novel cytokine and growth factor mediated pathways involved in late development of the collecting system and nephron. To specifically analyze the morphogenetic processes controlling renal tubulogenesis in spinal cord-induced metanephric mesenchyme, the model was analyzed from transcriptomic, anatomic, and biochemical perspectives to arrive at a characterization of in vitro nephrogenesis permissive of perturbation. Analysis of multiple nephrogenesis data sets identified regulatory mechanisms in a series of temporal networks. A screen of putative tubulogenesis regulating signaling pathways identified in transcriptomic analyses was performed. PKA activity was found to regulate morphogenesis of the renal vesicle, with sustained activity of the enzyme preventing tubular morphogenesis. Microarray analysis confirmed PKA activity prevented progression of development from the renal vesicle stage of morphogenesis. The Wnt signaling pathway was implicated and confirmed to upregulated by PKA signaling. Inhibition of the Wnt pathway rescued the PKA mediated disruption of tubulogenesis. This systems level analysis highlights novel early and late mechanisms of renal tubular morphogenesis