DPYSL3 modulates mitosis, migration, and epithelial-to-mesenchymal transition in claudin-low breast cancer

Significance Mass spectrometry-based proteogenomics of patient-derived xenografts (PDXs) identified dihydropyrimidinase-like-3 (DPYSL3) as a multilevel (RNA/protein/phosphoprotein) expression outlier specific to a claudin-low (CLOW) PDX. DPYSL3 has established functions in neural cell migration and axon outgrowth but is understudied in breast cancer. Here, we demonstrate that loss of DPYSL3 promotes cell-cycle arrest, multinucleation, and collapse of the vimentin microfilament network associated with increased phospho-vimentin. DPYSL3 is also a negative regulator of p21-activated kinase (PAK) and suppresses epithelial-to-mesenchymal transition (EMT). In turn, EMT regulators induce DPYSL3, suggesting that DPYSL3 provides negative feedback on EMT. DPYSL3 therefore serves as a biomarker for CLOW tumors that exhibit PAK-dependent motility and EMT and is also susceptible to therapeutic approaches that promote vimentin phosphorylation during mitosis.
A Clinical Proteomic Tumor Analysis Consortium (CPTAC) proteogenomic analysis prioritized dihydropyrimidinase-like-3 (DPYSL3) as a multilevel (RNA/protein/phosphoprotein) expression outlier specific to the claudin-low (CLOW) subset of triple-negative breast cancers. A PubMed informatics tool indicated a paucity of data in the context of breast cancer, which further prioritized DPYSL3 for study. DPYSL3 knockdown in DPYSL3-positive (DPYSL3+) CLOW cell lines demonstrated reduced proliferation, yet enhanced motility and increased expression of epithelial-to-mesenchymal transition (EMT) markers, suggesting that DPYSL3 is a multifunctional signaling modulator. Slower proliferation in DPYSL3-negative (DPYSL3−) CLOW cells was associated with accumulation of multinucleated cells, indicating a mitotic defect that was associated with a collapse of the vimentin microfilament network and increased vimentin phosphorylation. DPYSL3 also suppressed the expression of EMT regulators SNAIL and TWIST and opposed p21 activated kinase 2 (PAK2)-dependent migration. However, these EMT regulators in turn induce DPYSL3 expression, suggesting that DPYSL3 participates in negative feedback on EMT. In conclusion, DPYSL3 expression identifies CLOW tumors that will be sensitive to approaches that promote vimentin phosphorylation during mitosis and inhibitors of PAK signaling during migration and EMT.