Identifying novel targets of oncogenic EGF receptor signaling in lung cancer through global phosphoproteomics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25404012", "kind": "science-record", "revision": 5, "content_hash": "sha256:d786c55693e338b1b405a7dc60a24f95bd55e0a530b86739dd1092a9632f1109", "created_at": "2026-11-01T15:40:07Z", "updated_at": "2026-11-01T18:47:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying novel targets of oncogenic EGF receptor signaling in lung cancer through global phosphoproteomics.", "doi": "10.1002/pmic.201400315", "pmid": "25404012", "authors": ["Xu Zhang", "Natalya Belkina", "Harrys Kishore Charles Jacob", "Tapan Maity", "Romi Biswas", "Abhilash Venugopalan", "Patrick G Shaw", "Min-Sik Kim", "Raghothama Chaerkady", "Akhilesh Pandey", "Udayan Guha"], "journal": "Proteomics", "year": 2015, "abstract": "Mutations in the epidermal growth factor receptor (EGFR) kinase domain occur in 10-30% of lung adenocarcinoma and are associated with tyrosine kinase inhibitor (TKI) sensitivity. We sought to identify the immediate direct and indirect phosphorylation targets of mutant EGFRs in lung adenocarcinoma. We undertook SILAC strategy, phosphopeptide enrichment, and quantitative MS to identify dynamic changes of phosphorylation downstream of mutant EGFRs in lung adenocarcinoma cells harboring EGFR(L858R) and EGFR(L858R/T790M) , the TKI-sensitive, and TKI-resistant mutations, respectively. Top canonical pathways that were inhibited upon erlotinib treatment in sensitive cells, but not in the resistant cells include EGFR, insulin receptor, hepatocyte growth factor, mitogen-activated protein kinase, mechanistic target of rapamycin, ribosomal protein S6 kinase beta 1, and Janus kinase/signal transducer and activator of transcription signaling. We identified phosphosites in proteins of the autophagy network, such as ULK1 (S623) that is constitutively phosphorylated in these lung adenocarcinoma cells; phosphorylation is inhibited upon erlotinib treatment in sensitive cells, but not in resistant cells. Finally, kinase-substrate prediction analysis from our data indicated that substrates of basophilic kinases from, AGC and Calcium and calmodulin-dependent kinase groups, as well as STE group kinases were significantly enriched and those of proline-directed kinases from, CMGC and Casein kinase groups were significantly depleted among substrates that exhibited increased phosphorylation upon EGF stimulation and reduced phosphorylation upon TKI inhibition. This is the first study to date to examine global phosphorylation changes upon erlotinib treatment of lung adenocarcinoma cells and results from this study provide new insights into signaling downstream of mutant EGFRs in lung adenocarcinoma. All MS data have been deposited in the ProteomeXchange with identifier PXD001101 (http://proteomecentral.proteomexchange.org/dataset/PXD001101).", "claims": [], "gaps": []}, "experiment": {"state": "partial", "objective": "The study used three-state SILAC quantitative phosphoproteomics; kinase-substrate enrichment and depletion were tested with Fisher’s exact test using Benjamini-Hochberg adjustment, and the source mass-spectrometry data were deposited in ProteomeXchange through PRIDE under dataset identifier PXD001101. 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These cells were cultured in RPMI SILAC media at 37°C, 5% CO2 and high hu", "gma-Aldrich, (St. Louis, MO). The cells were passaged at least five times and screened for labelin", ".67and 1.5) at 5 minutes of EGF treatment of HeLa cells based on data published by Olsen et. a"], "order_basis": "paper_text_order:2470", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["s and screened for labeling efficiency using mass spectrometry. Upon completion of labeling, cells were exp"], "order_basis": "paper_text_order:3134", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["rom lysates of each state were combined. For Western blot based validation experiments unlabelled cell", "ting InformationSupplementary Figure S1. (A) Western blot analysis of lysates from H3255 and H1975 sho", "overexpression of EGFRL858R in H3255 cells. Western blots were probed with EGFRL858R- specific (detect", "cognizes both mutant and wild-type EGFR. (B) Western blot analysis of phosphotyrosine (4G10, Millipore"], "order_basis": "paper_text_order:4188", "id": "assay:3"}]}