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Wnt signaling generates patterns in all embryos, from flies to humans, and controls cell fate, proliferation, and metabolic homeostasis. Inappropriate Wnt pathway activation results in diseases, including colorectal cancer. The Adenomatous polyposis coli (APC) tumor suppressor gene encodes a multifunctional protein that is an essential regulator of Wnt signaling and cytoskeletal organization. While progress has been made in defining the role of APC in a normal cellular context, there are still significant gaps in our understanding of APC-dependent cellular function and dysfunction. We expanded the APC-associated protein network using a combination of genetics and a proteomic technique called Two-dimensional Difference Gel Electrophoresis (2D-DIGE). We show that loss of APC2 causes protein isoform changes reflecting misregulation of post-translational modifications (PTMs), which are not dependent on β-cat transcriptional activity. Mass spectrometry revealed that proteins involved in metabolic and biosynthetic pathways, protein synthesis and degradation, and cell signaling are affected by the loss of APC2. We demonstrate that changes in phosphorylation partially account for the altered PTMs in APC mutants, suggesting that APC mutants affect other types of PTM. Finally, through this approach Aminopeptidase P was identified as a new regulator of β-catenin abundance in Drosophila embryos. This study provides new perspectives on APC's cellular effects that may lead to a richer understanding of APC's role in development.

Proteomic analysis reveals APC-dependent post translational modifications and identifies a novel regulator of β-catenin