Genes involved in TGFβ1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map

Background: Understanding how mesenchymal cells arise from epithelial cells could have a strong impact in unveiling mechanisms of epithelial cell plasticity underlying kidney regeneration and repair. In primary human tubular epithelial cells (HUTEC) under different TGF beta 1 concentrations we had observed epithelial-to-mesenchymal transition (EMT) but not epithelial-myofibroblast transdifferentiation. We hypothesized that the process triggered by TGF beta 1 could be a dedifferentiation event. The purpose of this study is to comprehensively delineate genetic programs associated with TGF beta 1-driven EMT in our in vitro model using gene expression profile on large-scale oligonucleotide microarrays. Results: In HUTEC under TGF beta 1 stimulus, 977 genes were found differentially expressed. Thirty genes were identified whose expression depended directly on TGF beta 1 concentration. By mapping the differentially expressed genes in the Human Interactome Map using Cytoscape software, we identified a single scale-free network consisting of 2630 interacting proteins and containing 449 differentially expressed proteins. We identified 27 hub proteins in the interactome with more than 29 edges incident on them and encoded by differentially expressed genes. The Gene Ontology analysis showed an excess of up-regulated proteins involved in biological processes, such as morphogenesis, cell fate determination and regulation of development, and the most up-regulated genes belonged to these categories. In addition, 267 genes were mapped to the KEGG pathways and 14 pathways with more than nine differentially expressed genes were identified. In our model, Smad signaling was not the TGF beta 1 action effector; instead, the engagement of RAS/ MAPK signaling pathway seems mainly to regulate genes involved in the cell cycle and proliferation/ apoptosis. Conclusion: Our present findings support the hypothesis that context-dependent EMT generated in our model by TGF beta 1 might be the outcome of a dedifferentiation. In fact: 1) the principal biological categories involved in the process concern morphogenesis and development; 2) the most up-regulated genes belong to these categories; and, finally, 3) some intracellular pathways are involved, whose engagement during kidney development and nephrogenesis is well known. These long-term effects of TGF beta 1 in HUTEC involve genes that are highly interconnected, thereby generating a scale-free network that we named the TGF beta 1 interactome, whose hubs represent proteins that may have a crucial role for HUTEC in response to TGF beta 1.