Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes

Martin Mehnert (), Rodolfo Ciuffa, Fabian Frommelt, Federico Uliana, Audrey Drogen, Kilian Ruminski, Matthias Gstaiger () and Ruedi Aebersold ()
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Martin Mehnert: Institute of Molecular Systems Biology
Rodolfo Ciuffa: Institute of Molecular Systems Biology
Fabian Frommelt: Institute of Molecular Systems Biology
Federico Uliana: Institute of Molecular Systems Biology
Audrey Drogen: Institute of Molecular Systems Biology
Kilian Ruminski: Institute of Molecular Systems Biology
Matthias Gstaiger: Institute of Molecular Systems Biology
Ruedi Aebersold: Institute of Molecular Systems Biology

Nature Communications, 2020, vol. 11, issue 1, 1-18

Abstract: Abstract Rapidly increasing availability of genomic data and ensuing identification of disease associated mutations allows for an unbiased insight into genetic drivers of disease development. However, determination of molecular mechanisms by which individual genomic changes affect biochemical processes remains a major challenge. Here, we develop a multilayered proteomic workflow to explore how genetic lesions modulate the proteome and are translated into molecular phenotypes. Using this workflow we determine how expression of a panel of disease-associated mutations in the Dyrk2 protein kinase alter the composition, topology and activity of this kinase complex as well as the phosphoproteomic state of the cell. The data show that altered protein-protein interactions caused by the mutations are associated with topological changes and affected phosphorylation of known cancer driver proteins, thus linking Dyrk2 mutations with cancer-related biochemical processes. Overall, we discover multiple mutation-specific functionally relevant changes, thus highlighting the extensive plasticity of molecular responses to genetic lesions.

Date: 2020
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DOI: 10.1038/s41467-020-17387-y

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