PXD015687

PXD015687 is an original dataset announced via ProteomeXchange.

Title	Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes
Description	With the rapidly increasing availability of genomic data and ensuing identification of disease associated mutations, the determination of molecular mechanisms by which such mutations affect biochemical processes and phenotypes remains a major challenge. In this study we developed and applied a multilayered proteomic workflow to explore how genetic lesions modulate the modular proteome to alter functional phenotypes. Using this workflow we determined how expression of a panel of disease-associated mutations in the Dyrk2 protein kinase altered the composition, topology and activity of the multifunctional protein complex assembled around Dyrk2 and the phosphoproteomic state of the respective cells. We found that the selected cancer-related Dyrk2 mutations caused, to a differing extent, disassembly of the catalytic kinase core complex and caused disruption of interactions within the Dyrk2 core or with other cellular modules. This is exemplified by the nuclear pore associated Y-complex which we identified as new interactor of Dyrk2. We further found that the altered protein-protein interactions caused by the mutations are associated with topological changes and with changes in posttranslational modifications in the mutated kinase modules. Finally, we observed that the expression of each tested cancer-related mutation created a specific phosphoproteomic footprint including altered phosphorylation of known cancer-associated proteins, thus linking Dyrk2 mutations with cancer-related biochemical processes. Overall we developed an integrated, multilayered proteomic workflow to study how specific genomic mutations affect the modular proteome. Applying it to mutations in the Dyrk2 kinase we discover multiple mutation-specific, significant, pleiotropic and functionally relevant changes, highlighting the large plasticity of molecular responses to genomic lesions. The established workflow is generically applicable and will contribute to a better understanding of the molecular mechanisms that translate genomic alterations into (disease) phenotypes.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:09:33.601.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Martin Mehnert
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	biotinylated residue; phosphorylated residue
Instrument	Orbitrap Fusion Lumos; LTQ Orbitrap XL; LTQ Orbitrap Elite; TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-03 01:35:50	ID requested
1	2020-07-21 22:37:36	announced
⏵ 2	2024-10-22 05:09:38	announced	2024-10-22: Updated project metadata.

10.1038/s41467-020-17387-y;

Mehnert M, Ciuffa R, Frommelt F, Uliana F, van Drogen A, Ruminski K, Gstaiger M, Aebersold R, Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes. Nat Commun, 11(1):3563(2020) [pubmed]

submitter keyword: Human, PRM, Dyrk2, SWATH-MS, DDA, cancer mutations

Ruedi Aebersold
contact affiliation	Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Switzerland and Faculty of Science, University of Zurich, Switzerland
contact email	aebersold@imsb.biol.ethz.ch
lab head
Martin Mehnert
contact affiliation	ETH Zurich
contact email	mehnert@imsb.biol.ethz.ch
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/07/PXD015687

PRIDE project URI

• PRIDE
  1. PXD015687
     1. Label: PRIDE project
     2. Name: Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes