Phosphoproteomics identifies PAK2-associated developmental modules in mouse embryos

The p21-activated kinases (PAKs) are conserved serine/threonine kinases that couple cytoskeletal dynamics to diverse cellular processes. Despite emerging roles for PAK2 in development and disease, its regulated phosphorylation programs remain poorly defined. Here, we performed quantitative phosphoproteomic profiling of WT and Pak2^-/- mouse embryos at embryonic day 9.5 and identified 151 differential phosphopeptide features, corresponding to 119 phosphosites and 116 PAK2-associated phosphoproteins. Differential events were predominantly downregulated and enriched for serine-proline motifs. Functional analyses highlighted modules involved in nuclear RNA processing, chromatin/DNA regulation, translation/RNA-binding, cytoskeletal signaling, and neurodevelopment. Finally, bulk RNA-seq and single-cell transcriptomic analyses integrated the genes encoding these phosphoproteins into cellular and developmental programs, providing transcriptomic context for the PAK2-associated post-translational events in early embryogenesis.