ArticleEBioMedicine2019
Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: Reanalysis of CPTAC ovarian cancer.
Article in EBioMedicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 26 citations in OpenAlex.
- KSDiffusion: conditional diffusion for kinase-specific phosphorylation site prediction under data-limited and imbalanced regimes.Briefings in bioinformatics · 2026Article
- Comprehensive Multiplatform Tyrosine Kinase Profiling Reveals Novel Actionable FGFR Aberrations across Sarcomas Affecting the Young.Molecular cancer therapeutics · 2026Article
- Kinase activities in pancreatic ductal adenocarcinoma with prognostic and therapeutic avenues.Molecular oncology · 2024Article
- Proteomic landscape of epithelial ovarian cancer.Nature communications · 2024Article
- Proteome-based molecular subtyping and therapeutic target prediction in gastric cancer.Molecular oncology · 2024Article
- Proteogenomic data and resources for pan-cancer analysis.Cancer cell · 2023Review
- Resistance prediction in high-grade serous ovarian carcinoma with neoadjuvant chemotherapy using data-independent acquisition proteomics and an ovary-specific spectral library.Molecular oncology · 2023Article
- GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins.Nucleic acids research · 2023Article
- Mass Spectrometry-Based Proteomics of Epithelial Ovarian Cancers: A Clinical Perspective.Molecular & cellular proteomics : MCP · 2023Review
- Principles of phosphoproteomics and applications in cancer research.The Biochemical journal · 2023Article
- Gene co-expression network analysis revealed novel biomarkers for ovarian cancer.Frontiers in genetics · 2022Article
- Comprehending the Proteomic Landscape of Ovarian Cancer: A Road to the Discovery of Disease Biomarkers.Proteomes · 2021Review
- Simplified and Unified Access to Cancer Proteogenomic Data.Journal of proteome research · 2021Article
- Recent Advances in Integrative Multi-Omics Research in Breast and Ovarian Cancer.Journal of personalized medicine · 2021Review
- Article
- Application of Proteomics in Cancer: Recent Trends and Approaches for Biomarkers Discovery.Frontiers in medicine · 2021Review
- Phosphoproteomics Reveals Key Regulatory Kinases and Modulated Pathways Associated with Ovarian Cancer Tumors.OncoTargets and therapy · 2020Article
- Article
- Re-assessment of the high-grade serous ovarian cancer phosphoproteome - Identification of kinase candidates in TCGA tumors for future clinical intervention.EBioMedicine · 2019Article
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMolecular subtyping of cancer aimed to predict patient overall survival (OS) and nominate drug targets for patient treatments is central to precision oncology. Owing to the rapid development of phosphoproteomics, we can now measure thousands of phosphoproteins in human cancer tissues. However, limited studies report how to analyse the complex phosphoproteomic data for cancer subtyping and to nominate druggable kinase candidates.
findingsIn this work, we reanalysed the phosphoproteomic data of high-grade serous ovarian cancer (HGSOC) from the Clinical Proteomic Tumour Analysis Consortium (CPTAC). Our analysis classified HGSOC into 5 major subtypes that were associated with different OS and appeared to be more accurate than that achieved with protein profiling. We provided a workflow to identify 29 kinases whose increased activities in tumours are associated with poor survival. The altered kinase signalling landscape of HGSOC included the PI3K/AKT/mTOR, cell cycle and MAP kinase signalling pathways. We also developed a "patient-specific" hierarchy of clinically actionable kinases and selected kinase inhibitors by considering kinase activation and kinase inhibitor selectivity.
interpretationOur study offered a global phosphoproteomics data analysis workflow to aid in cancer molecular subtyping, determining phosphorylation-based cancer hallmarks and facilitating nomination of kinase inhibition in cancer.
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