Unbiased Proteomic and Phosphoproteomic Analysis Identifies Response Signatures and Novel Susceptibilities After Combined MEK and mTOR Inhibition in BRAFV600E Mutant Glioma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34298159", "kind": "science-record", "revision": 7, "content_hash": "sha256:91e91f68c1ce4eb6b3347b68e370924f28e5a4efc07b61ac6831d76271636bd0", "created_at": "2026-11-01T15:41:44Z", "updated_at": "2026-11-01T22:04:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Unbiased Proteomic and Phosphoproteomic Analysis Identifies Response Signatures and Novel Susceptibilities After Combined MEK and mTOR Inhibition in BRAFV600E Mutant Glioma.", "doi": "10.1016/j.mcpro.2021.100123", "pmid": "34298159", "authors": ["Micah J Maxwell", "Antje Arnold", "Heather Sweeney", "Lijun Chen", "Tung-Shing M Lih", "Michael Schnaubelt", "Charles G Eberhart", "Jeffrey A Rubens", "Hui Zhang", "David J Clark", "Eric H Raabe"], "journal": "Molecular & cellular proteomics : MCP", "year": 2021, "abstract": "The mitogen-activated protein kinase pathway is one of the most frequently altered pathways in cancer. It is involved in the control of cell proliferation, invasion, and metabolism, and can cause resistance to therapy. A number of aggressive malignancies, including melanoma, colon cancer, and glioma, are driven by a constitutively activating missense mutation (V600E) in the v-Raf murine sarcoma viral oncogene homolog B (BRAF) component of the pathway. Mitogen-activated protein kinase kinase (MEK) inhibition is initially effective in targeting these cancers, but reflexive activation of mammalian target of rapamycin (mTOR) signaling contributes to frequent therapy resistance. We have previously demonstrated that combination treatment with the MEK inhibitor trametinib and the dual mammalian target of rapamycin complex 1/2 inhibitor TAK228 improves survival and decreases vascularization in a BRAFV600E mutant glioma model. To elucidate the mechanism of action of this combination therapy and understand the ensuing tumor response, we performed comprehensive unbiased proteomic and phosphoproteomic characterization of BRAFV600E mutant glioma xenografts after short-course treatment with trametinib and TAK228. We identified 13,313 proteins and 30,928 localized phosphosites, of which 12,526 proteins and 17,444 phosphosites were quantified across all samples (data available via ProteomeXchange; identifier PXD022329). We identified distinct response signatures for each monotherapy and combination therapy and validated that combination treatment inhibited activation of the mitogen-activated protein kinase and mTOR pathways. Combination therapy also increased apoptotic signaling, suppressed angiogenesis signaling, and broadly suppressed the activity of the cyclin-dependent kinases. In response to combination therapy, both epidermal growth factor receptor and class 1 histone deacetylase proteins were activated. This study reports a detailed (phospho)proteomic analysis of the response of BRAFV600E mutant glioma to combined MEK and mTOR pathway inhibition and identifies new targets for the development of rational combination therapies for BRAF-driven tumors.", "claims": [{"id": "claim-data-access", "statement": "All the MS proteomics data (both global proteome and phosphoproteome), including raw MS data, processed peak lists, and respective search results have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) (70) via the PRIDE (71) partner repository with the dataset identifier PXD022329.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34298159", "locator": "sections[23] \"Data Availability\" paragraph 2", "quote": "All the MS proteomics data (both global proteome and phosphoproteome), including raw MS data, processed peak lists, and respective search results have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) (70) via the PRIDE (71) partner repository with the dataset identifier PXD022329."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:34298159"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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