Quantitative Proteomic Analysis in Alveolar Type II Cells Reveals the Different Capacities of RAS and TGF-β to Induce Epithelial-Mesenchymal Transition.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33869273", "kind": "science-record", "revision": 8, "content_hash": "sha256:e3dd9677f31ccbd564f8935c76603396fbc18edc53733229753a5c2fb7d1ac66", "created_at": "2026-11-01T15:41:32Z", "updated_at": "2026-11-01T22:46:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative Proteomic Analysis in Alveolar Type II Cells Reveals the Different Capacities of RAS and TGF-β to Induce Epithelial-Mesenchymal Transition.", "doi": "10.3389/fmolb.2021.595712", "pmid": "33869273", "authors": ["Yilu Zhou", "Charlotte Hill", "Liudi Yao", "Juanjuan Li", "David Hancock", "Julian Downward", "Mark G Jones", "Donna E Davies", "Rob M Ewing", "Paul Skipp", "Yihua Wang"], "journal": "Frontiers in molecular biosciences", "year": 2021, "abstract": "Alveolar type II (ATII) epithelial cells function as stem cells, contributing to alveolar renewal, repair and cancer. Therefore, they are a highly relevant model for studying a number of lung diseases, including acute injury, fibrosis and cancer, in which signals transduced by RAS and transforming growth factor (TGF)-β play critical roles. To identify downstream molecular events following RAS and/or TGF-β activation, we performed proteomic analysis using a quantitative label-free approach (LC-HDMSE) to provide in-depth proteome coverage and estimates of protein concentration in absolute amounts. Data are available via ProteomeXchange with identifier PXD023720. We chose ATIIER:KRASV12 as an experimental cell line in which RAS is activated by adding 4-hydroxytamoxifen (4-OHT). Proteomic analysis of ATII cells treated with 4-OHT or TGF-β demonstrated that RAS activation induces an epithelial-mesenchymal transition (EMT) signature. In contrast, under the same conditions, activation of TGF-β signaling alone only induces a partial EMT. EMT is a dynamic and reversible biological process by which epithelial cells lose their cell polarity and down-regulate cadherin-mediated cell-cell adhesion to gain migratory properties, and is involved in embryonic development, wound healing, fibrosis and cancer metastasis. Thus, these results could help to focus research on the identification of processes that are potentially driving EMT-related human disease.", "claims": [{"id": "claim-method", "statement": "The limma package (v. 3_34.2) was utilized to detect differentially expressed proteins (DEPs) (Ritchie et al., 2015).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33869273", "locator": "sections[7] \"Proteomic Sample Normalization and Imputation\" paragraph 4", "quote": "The limma package (v. 3_34.2) was utilized to detect differentially expressed proteins (DEPs) (Ritchie et al., 2015)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD023720.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33869273", "locator": "sections[7] \"Proteomic Sample Normalization and Imputation\" paragraph 4", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD023720."}], "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:33869273"], "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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"P55265, Q08722, Q14258, Q01629"], ["Hallmark reactive oxygen species pathway", "−4.809", "NQO1, TXN, OXSR1", "3/49", "P15559, P10599, O95747"]], "row_count": 15, "column_count": 5, "numeric_cells": 46, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33869273:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:384dd02f88a870f00eb3251980b378853662773e9058c98f262ba936ebdf76b5", "bytes": 1385, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T2", "version": null, "note": "Hallmark pathways identified using Metascape (Metascape.com) for differentially expressed proteins between control and TGF-β-treated ATIIER:KRASV12 cells.", "structure": {"pmcid": "PMC8048883", "section_index": 12, "section_title": "Transforming Growth Factor-β Does Not Induce a Hallmark Epithelial–Mesenchymal Transition in 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"5/200", "P00558, P14618, P11216, Q15582, P10599"], ["Hallmark DNA repair", "−1.763", "POLR2H, RALA, ALYREF, SF3A3", "4/150", "P52434, P11233, Q86V81, Q12874"], ["Hallmark myc targets v1", "−1.475", "EEF1B2, KPNB1, PGK1, SYNCRIP", "4/150", "P24534, Q14974, P00558, O60506"], ["Hallmark epithelial-mesenchymal transition", "−0.916", "THBS1,ITGAV, TGFBI", "3/200", "P07996, P06756, Q15582"]], "row_count": 10, "column_count": 5, "numeric_cells": 31, "header_rows": 1, "locator": "section[12]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:33869273:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:eda670d198de7ce95c711c388ba20c452afbdf694e7720e8d85cc0208c5be4e2", "bytes": 2403, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T3", "version": null, "note": "Hallmark pathways identified using Metascape (Metascape.com) for differentially 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