ArticleNature biotechnology2020
Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring.
Article in Nature biotechnology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 113 citations in OpenAlex.
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- A Constellation of Fluorescent Biosensors to Illuminate the Galaxy of Protein Kinases.Chembiochem : a European journal of chemical biology · 2026Review
- Surfaceome Capture by Multiplex Biotinylation Enables Enhanced Identification of Cell Surface Proteins by Mass Spectrometry.Molecular & cellular proteomics : MCP · 2026Article
- Benchmarking EGF signaling pathway inference using phosphoproteomics and kinase-substrate interactions.Nature communications · 2026Article
- High-Grade Serous Ovarian Carcinoma in the Genomics Era: Current Applications, Challenges and Future Directions.International journal of molecular sciences · 2026Review
- Computational Approaches for Pathway-Centric Analysis of Protein Post-Translational Modifications.Proteomics · 2025Review
- SFX-01 is therapeutic against myeloproliferative disorders caused by activating mutations in Shp2.EMBO molecular medicine · 2025Article
- Comprehensive evaluation of phosphoproteomic-based kinase activity inference.Nature communications · 2025Article
- Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites.Nature communications · 2025Article
- Phosphoproteomics identifies determinants of PAK inhibitor sensitivity in leukaemia cells.Cell communication and signaling : CCS · 2025Article
- Weighted Gene Networks Derived from Multi-Omics Reveal Core Cancer Genes in Lung Cancer.Biology · 2025Article
- Article
- Functional Pathway Inference Analysis (FPIA).Methods in molecular biology (Clifton, N.J.) · 2025Article
- A class I PI3K signalling network regulates primary cilia disassembly in normal physiology and disease.Nature communications · 2024Article
- The ric-8b protein (resistance to inhibitors of cholinesterase 8b) is key to preserving contractile function in the adult heart.The Journal of biological chemistry · 2024Article
- Phosphoproteomic profiling of early rheumatoid arthritis synovium reveals active signalling pathways and differentiates inflammatory pathotypes.Arthritis research & therapy · 2024Article
- Application of omics in the diagnosis, prognosis, and treatment of acute myeloid leukemia.Biomarker research · 2024Review
- An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors.Molecular systems biology · 2024Article
- Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis.Nature communications · 2024Article
- Efferocyte-Derived MCTRs Metabolically Prime Macrophages for Continual Efferocytosis via Rac1-Mediated Activation of Glycolysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Understanding how oncogenic mutations rewire regulatory-protein networks is important for rationalizing the mechanisms of oncogenesis and for individualizing anticancer treatments. We report a chemical phosphoproteomics method to elucidate the topology of kinase-signaling networks in mammalian cells. We identified >6,000 protein phosphorylation sites that can be used to infer >1,500 kinase-kinase interactions and devised algorithms that can reconstruct kinase network topologies from these phosphoproteomics data. Application of our methods to primary acute myeloid leukemia and breast cancer tumors quantified the relationship between kinase expression and activity, and enabled the identification of hitherto unknown kinase network topologies associated with drug-resistant phenotypes or specific genetic mutations. Using orthogonal methods we validated that PIK3CA wild-type cells adopt MAPK-dependent circuitries in breast cancer cells and that the kinase TTK is important in acute myeloid leukemia. Our phosphoproteomic signatures of network circuitry can identify kinase topologies associated with both phenotypes and genotypes of cancer cells.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.