Multiplexed profiling of kinase interactomes quantifies cellular network plasticity

Golkowski, M.; Lius, A.; Sapre, T. S.; Lau, H.-T.; Moreno, T.; Maly, D. J.; Ong, S.-E.

doi:10.1101/2021.09.14.460283

Home/Archive/bioRxiv

bioRxiv · 10.1101/2021.09.14.460283

Multiplexed profiling of kinase interactomes quantifies cellular network plasticity

Golkowski, M.·Lius, A.·Sapre, T. S.·Lau, H.-T.·Moreno, T.·Maly, D. J.·Ong, S.-E.

View original source ↗Export metadata ↓

Abstract

Cells utilize protein-protein interaction (PPI) networks to receive, transduce, and respond to stimuli. Interaction network rewiring drives devastating diseases like cancers, making PPIs attractive targets for pharmacological intervention. Kinases are druggable nodes in PPI networks but high-throughput proteomics approaches to quantify disease-associated kinome PPI rewiring are lacking. We introduce kinobead competition and correlation analysis (Ki-CCA), a chemoproteomics approach to simultaneously map hundreds of endogenous kinase PPIs. We identified 2,305 PPIs of 300 kinases across 18 diverse cancer lines, quantifying the high plasticity of interaction networks between cancer types, signaling, and phenotypic states; this database of dynamic kinome PPIs provides deep insights into cancer cell signaling. We discovered an AAK1 complex promoting epithelial-mesenchymal transition and drug resistance, and depleting its components sensitized cells to targeted therapy. Ki-CCA enables rapid and highly multiplexed mapping of kinome PPIs in native cell and tissue lysates, without epitope tagged baits, protein labeling, or antibodies.

Explore related subjects

biochemistry Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Golkowski, M., Lius, A., Sapre, T. S., Lau, H.-T., Moreno, T., Maly, D. J., Ong, S.-E.. 2021-09-15. Multiplexed profiling of kinase interactomes quantifies cellular network plasticity. https://doi.org/10.1101/2021.09.14.460283

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

The structures of two intermediates en route to DNA repair within a (6-4) photolyase

Pyrimidine (6-4) pyrimidone photoproducts (6-4PPs) are mutagenic DNA lesions produced when UV light crosslinks two adjacent pyrimidine bases. These lesions must be repaired to maintain genome integrity, a function executed by the (6-4) photolyase enzymes. This repair chemistry is complex, involving the transfer of a hydroxyl group from one base to another, accompanied or followed by cleavage of an interbase bond. It remains unclear how the enzyme orchestrates this reaction. Typically, models invoke a stepwise process in which an oxetane intermediate is transiently populated, but despite over thirty years of investigation, such an intermediate has never been definitively observed. Conducting dose-controlled X-ray crystallography on the (6-4) photolyase from Vibrio cholerae, we observed the transformation of 6-4PP into an oxetane species. Furthermore, we identified a previously unanticipated hemi-cleaved intermediate. The progressive transformation of 6-4PP into oxetane, hemi-cleaved, and fully repaired species requires a reexamination of the existing models of DNA repair by (6-4) photolyases.

biochemistry↗

bioRxiv2026

Endothelial protein C receptor is an entry receptor for Langya virus

Langya virus (LayV) was recently discovered in infected individuals with febrile illness and classified as a Parahenipavirus, a group of poorly understood pathogens. LayV is distantly related to Nipah henipavirus which causes recurring outbreaks with case fatality rates reaching up to 90%. No vaccines or therapeutics are approved for use in humans for any parahenipavirus or henipavirus despite their broad geographic distribution and pandemic potential. Here, we discovered that human endothelial protein C receptor (EPCR) is an entry receptor for LayV and that the tetrameric LayV attachment glycoprotein (G) binds EPCR avidly. We reveal the molecular basis of LayV G recognition of the EPCR receptor and provide a blueprint of the determinants of receptor ortholog usage. We found that human and shrew EPCR orthologs promote cell entry of LayV and of the closely related Mojiang pseudoviruses. These results along with the detection of several Parahenipaviruses in shrews set these pathogens apart from Henipaviruses, which use Pteropid fruit bats as reservoir hosts. Our data support future surveillance efforts, by enabling prediction of EPCR utilization among newly discovered Parahenipaviruses, and the development and evaluation of countermeasures targeting this emerging group of human pathogens.

biochemistry↗

bioRxiv2026

RNA-targeted aminopyridine compounds provide a new antifungal strategy

While RNA is an emerging therapeutic target class, progress is limited by a shortage of well-defined targets in which ligand binding is coupled to measurable function. The group I intron, a self-splicing ribozyme essential in fungal mitochondria but absent from humans, offers both a tractable platform for exploring first principles of small molecule-RNA targeting and a selective antifungal target. We recalibrated an intron-splicing assay to approximate cellular conditions and performed an extensive, cryo-EM-guided structure-activity relationship campaign against the Candida albicans mtLSU intron. Ligands containing a flexible diamine outperformed conformationally constrained analogues, suggesting a general principle for engaging dynamic RNA surfaces and yielding lead aminopyridine 56 (IC 21.6 nM). Compound 56 synergizes with amphotericin B against C. albicans, suggesting a path for combination therapies. RT-qPCR confirmed direct target engagement in cells. This work establishes the fungal group I intron as a viable, mechanistically distinct antifungal target and a model platform for RNA-targeted discovery.

biochemistry↗