PXD039859-1
PXD039859 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis |
| Description | Aberrant signaling pathway activity is a hallmark of tumorigenesis and progression, which has guided targeted inhibitor design for over 30 years. Yet, adaptive resistance mechanisms, induced by rapid, context-specific signaling network rewiring, continue to challenge therapeutic efficacy. By leveraging progress in proteomic technologies and network-based methodologies over the past decade we developed VESPA, an algorithm designed to elucidate mechanisms of cell response and adaptation to drug perturbations, and used it to analyze 7-point phosphoproteomic time series from colorectal cancer cells treated with clinically-relevant inhibitors and control media. Interrogation of tumor-specific enzyme/substrate interactions accurately inferred kinase and phosphatase activity, based on their inferred substrate phosphorylation state, effectively accounting for signal cross-talk and sparse phosphoproteome coverage. The analysis elucidated time-dependent signaling pathway response to each drug perturbation and, more importantly, cell adaptive response and rewiring that was experimentally confirmed by CRISPRko assays, suggesting broad applicability to cancer and other diseases. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-03-01 |
| AnnouncementXML | Submission_2024-03-01_02:27:09.906.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | George Rosenberger |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Phospho |
| Instrument | Orbitrap Fusion Lumos |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2023-02-04 13:19:12 | ID requested | |
| ⏵ 1 | 2024-03-01 02:27:10 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Data-independent acquisiton, DIA, OpenSWATH, VESPA, Network inference, Signaling, Machine learning, VIPER |
Contact List
| Andrea Califano | |
|---|---|
| contact affiliation | Columbia University, NY, USA |
| contact email | ac2248@cumc.columbia.edu |
| lab head | |
| George Rosenberger | |
| contact affiliation | Columbia University |
| contact email | gr2578@cumc.columbia.edu |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| 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://massive.ucsd.edu/v05/MSV000091204/ |
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