Proteomic profiling of senescent human diploid fibroblasts treated with gamma-tocotrienol.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30497457", "kind": "science-record", "revision": 6, "content_hash": "sha256:351dab985d0b62ea6ecc1ab330803fadecf3b284d55fed5e5350ce026d22b1d0", "created_at": "2026-11-01T15:40:39Z", "updated_at": "2026-11-01T21:21:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic profiling of senescent human diploid fibroblasts treated with gamma-tocotrienol.", "doi": "10.1186/s12906-018-2383-6", "pmid": "30497457", "authors": ["Jen-Kit Tan", "Faizul Jaafar", "Suzana Makpol"], "journal": "BMC complementary and alternative medicine", "year": 2018, "abstract": "BACKGROUND: Replicative senescence of human diploid fibroblasts (HDFs) has been used as a model to study mechanisms of cellular aging. Gamma-tocotrienol (γT3) is one of the members of vitamin E family which has been shown to increase proliferation of senescent HDFs. However, the modulation of protein expressions by γT3 in senescent HDFs remains to be elucidated. Therefore, this study aimed to determine the differentially expressed proteins (DEPs) in young and senescent HDFs; and in vehicle- and γT3-treated senescent HDFs using label-free quantitative proteomics.\nMETHODS: Whole proteins were extracted and digested in-gel with trypsin. Peptides were detected by Orbitrap liquid chromatography mass spectrometry. Mass spectra were identified and quantitated by MaxQuant software. The data were further filtered and analyzed statistically using Perseus software to identify DEPs. Functional annotations of DEPs were performed using Panther Classification System.\nRESULTS: A total of 1217 proteins were identified in young and senescent cells, while 1218 proteins in vehicle- and γT3-treated senescent cells. 11 DEPs were found in young and senescent cells which included downregulation of platelet-derived growth factor (PDGF) receptor beta and upregulation of tubulin beta-2A chain protein expressions in senescent cells. 51 DEPs were identified in vehicle- and γT3-treated senescent cells which included upregulation of 70 kDa heat shock protein, triosephosphate isomerase and malate dehydrogenase protein expressions in γT3-treated senescent cells.\nCONCLUSIONS: PDGF signaling and cytoskeletal structure may be dysregulated in senescent HDFs. The pro-proliferative effect of γT3 on senescent HDFs may be mediated through the stimulation of cellular response to stress and carbohydrate metabolism. The expressions and roles of these proteins in relation to cellular senescence are worth further investigations. Data are available via ProteomeXchange with identifier PXD009933.", "claims": [{"id": "claim-method", "statement": "The expressions of proteins between 2 groups were compared using 2-sample T-test with p value set at < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30497457", "locator": "sections[8] \"Statistical analysis\" paragraph 2", "quote": "The expressions of proteins between 2 groups were compared using 2-sample T-test with p value set at < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomic data have been deposited to the ProteomeXchange Consortium via the PRIDE [21] partner repository with the dataset identifier PXD009933.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30497457", "locator": "sections[9] \"Pathway analysis\" paragraph 3", "quote": "The mass spectrometry proteomic data have been deposited to the ProteomeXchange Consortium via the PRIDE [21] partner repository with the dataset identifier PXD009933."}], "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:30497457"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD009933"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD009933"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30497457", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12906-018-2383-6", "sha256": 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with the dataset identifier PXD009933.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomic data have been deposited to the ProteomeXchange Consortium via the PRIDE [21] partner repository with the dataset identifier PXD009933.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "proteomic analysis of gamma-tocotienol(GT3)-treated human diploid fibroblasts (HDFs)", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30497457:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:754381659d4ab4ec7e3653c2994c2f9f09151b8576f328725573fb46139ae30c", 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"Inactive tyrosine-protein kinase 7 (PTK7)"], ["P09619", "Platelet-derived growth factor receptor beta (PDGFRB)"]], "row_count": 14, "column_count": 2, "numeric_cells": 14, "header_rows": 1, "locator": "section[11]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:30497457:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:380fd0e08dc311117fd0d12c040eb4718e6aeed0e7bacd847268748bc36f33dd", "bytes": 3372, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#Tab2", "version": null, "note": "List of differentially expressed proteins in vehicle- and γT3-treated senescent cells", "structure": {"pmcid": "PMC6267793", "section_index": 11, "section_title": "LFQ analysis", "row_count": 54, "column_count": 2}, "table": {"label": "Table 2", "caption": "List of differentially expressed proteins in vehicle- and γT3-treated senescent cells", "rows": [["Protein ID", "Protein name (symbol)"], ["Upregulated"], ["O00487", "26S proteasome non-ATPase regulatory subunit 14 (PSMD14)"], ["P08865", "40S ribosomal protein SA (RPSA)"], ["Q969Q0", "60S ribosomal protein L36a-like (RPL36AL)"], ["P30533", "Alpha-2-macroglobulin receptor-associated protein (LRPAP1)"], ["P40222", "Alpha-taxilin (TXLNA)"], ["P07355;A6NMY6", "Annexin A2 (ANXA2);Putative annexin A2-like protein (ANXA2P2)"], ["P08758", "Annexin A5 (ANXA5)"], ["Q9NUU7;Q9UMR2", "ATP-dependent RNA helicase DDX19A (DDX19A);ATP-dependent RNA helicase DDX19B (DDX19B)"], ["Q05682", "Caldesmon (CALD1)"], ["P17612;P22694", "cAMP-dependent protein kinase catalytic subunit alpha (PRKACA);cAMP-dependent protein kinase catalytic subunit beta (PRKACB)"], ["P17812", "CTP synthase 1 (CTPS1)"], ["P54886", "Delta-1-pyrroline-5-carboxylate synthase (ALDH18A1)"], ["Q9NZN3", "EH domain-containing protein 3 (EHD3)"], ["O94905", "Erlin-2 (ERLIN2)"], ["O75822", "Eukaryotic translation initiation factor 3 subunit J (EIF3J)"], ["Q9Y262", "Eukaryotic translation initiation factor 3 subunit L (EIF3L)"], ["P14324", "Farnesyl pyrophosphate synthase (FDPS)"], ["P14314", "Glucosidase 2 subunit beta (PRKCSH)"], ["Q06210", "Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (GFPT1)"], ["Q9UBQ7", "Glyoxylate reductase/hydroxypyruvate reductase (GRHPR)"], ["P0DMV9;P0DMV8", "Heat shock 70 kDa protein 1B (HSPA71B);Heat shock 70 kDa protein 1A (HSPA71A)"], ["Q14103", "Heterogeneous nuclear ribonucleoprotein D0 (HNRNPD)"], ["O14979", "Heterogeneous nuclear ribonucleoprotein D-like (HNRNDL)"], ["P31942", "Heterogeneous nuclear ribonucleoprotein H3 (HNRNH3)"], ["P22626", "Heterogeneous nuclear ribonucleoproteins A2/B1 (HNRNPA2B1)"], ["Q16850", "Lanosterol 14-alpha demethylase (CYP51A1)"], ["Q96AG4", "Leucine-rich repeat-containing protein 59 (LRRC59)"], ["P40926", "Malate dehydrogenase, mitochondrial (MDH2)"], ["P29966", "Myristoylated alanine-rich C-kinase substrate (MARCKS)"], ["Q96AY3", "Peptidyl-prolyl cis-trans isomerase FKBP10 (FKBP10)"], ["P48739", "Phosphatidylinositol transfer protein beta isoform (PITPNB)"], ["O60568", "Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 (PLOD3)"], ["Q99623", "Prohibitin-2 (PHB2)"], ["Q86UE4", "Protein LYRIC (MTDH)"], ["Q96M27", "Protein PRRC1 (PRRC1)"], ["Q15436", "Protein transport protein Sec23A (SEC23A)"], ["P35241", "Radixin (RDX)"], ["Q9UN86", "Ras GTPase-activating protein-binding protein 2 (G3BP2)"], ["Q15019", "Septin-2 (SEPT2)"], ["P62136", "Serine/threonine-protein phosphatase PP1-alpha catalytic subunit (PPP1CA)"], ["Q9BWM7", "Sideroflexin-3 (SFXN3)"], ["P08240", "Signal recognition particle receptor subunit alpha (SRPRA)"], ["O43765", "Small glutamine-rich tetratricopeptide repeat-containing protein alpha (SGTA)"], ["Q9Y5X3", "Sorting nexin-5 (SNX5)"], ["Q8WZ42", "Titin (TTN)"], ["P60174", "Triosephosphate isomerase (TPI1)"], ["P09493", "Tropomyosin alpha-1 chain (TPM1)"], ["P06753", "Tropomyosin alpha-3 chain 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