Comparative proteoinformatics revealed the essentials of SDS impact on HaCaT keratinocytes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36509991", "kind": "science-record", "revision": 4, "content_hash": "sha256:7036827b26dbdeb278615e16c609a83d081866cd452b6e9a8722e439aa986dfc", "created_at": "2026-11-01T19:01:01Z", "updated_at": "2026-11-01T22:50:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparative proteoinformatics revealed the essentials of SDS impact on HaCaT keratinocytes.", "doi": "10.1038/s41598-022-25934-4", "pmid": "36509991", "authors": ["Timur Shkrigunov", "Yulia Kisrieva", "Natalia Samenkova", "Olesya Larina", "Victor Zgoda", "Alexander Rusanov", "Daniil Romashin", "Natalia Luzgina", "Irina Karuzina", "Andrey Lisitsa", "Natalia Petushkova"], "journal": "Scientific reports", "year": 2022, "abstract": "There is no direct evidence supporting that SDS is a carcinogen, so to investigate this fact, we used HaCaT keratinocytes as a model of human epidermal cells. To reveal the candidate proteins and/or pathways characterizing the SDS impact on HaCaT, we proposed comparative proteoinformatics pipeline. For protein extraction, the performance of two sample preparation protocols was assessed: 0.2% SDS-based solubilization combined with the 1DE-gel concentration (Protocol 1) and osmotic shock (Protocol 2). As a result, in SDS-exposed HaCaT cells, Protocol 1 revealed 54 differentially expressed proteins (DEPs) involved in the disease of cellular proliferation (DOID:14566), whereas Protocol 2 found 45 DEPs of the same disease ID. The 'skin cancer' term was a single significant COSMIC term for Protocol 1 DEPs, including those involved in double-strand break repair pathway (BIR, GO:0000727). Considerable upregulation of BIR-associated proteins MCM3, MCM6, and MCM7 was detected. The eightfold increase in MCM6 level was verified by reverse transcription qPCR. Thus, Protocol 1 demonstrated high effectiveness in terms of the total number and sensitivity of MS identifications in HaCaT cell line proteomic analysis. The utility of Protocol 1 was confirmed by the revealed upregulation of cancer-associated MCM6 in HaCaT keratinocytes induced by non-toxic concentration of SDS. Data are available via ProteomeXchange with identifier PXD035202.", "claims": [{"id": "claim-method", "statement": "One-way analysis of variance was performed using the Tukey HSD test for the multiple comparisons of mean values69.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36509991", "locator": "sections[15] \"Reverse transcription quantitative PCR\" paragraph 2", "quote": "One-way analysis of variance was performed using the Tukey HSD test for the multiple comparisons of mean values69."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analysed during the current study are available in the ProteomeXchange repository, http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD035202.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36509991", "locator": "sections[23] \"notes\" paragraph 1", "quote": "The datasets generated and/or analysed during the current study are available in the ProteomeXchange repository, http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD035202."}], "state": "complete"}, {"id": "claim-target-result", "statement": "SDS exposure increased the MCM6 protein level eightfold in HaCaT keratinocytes, and this increase was verified by reverse transcription qPCR.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36509991", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The eightfold increase in MCM6 level was verified by reverse transcription qPCR."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "SDS exposure increased the MCM6 protein level eightfold in HaCaT keratinocytes, and this increase was verified by reverse transcription qPCR.", "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:36509991"], "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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Thus, Protocol 1 demonstrated high effectiv", "CM6, reverse transcription quantitative PCR (RT-qPCR) analysis was performed (Fig. 6).Figure 6The", ", reverse transcription quantitative PCR (RT-qPCR) analysis was performed (Fig. 6).Figure 6The"], "order_basis": "paper_text_order:1105", "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": 0.99, "evidence": ["ity of MS identifications in HaCaT cell line proteomic analysis. The utility of Protocol 1 was conf", "ple preparation is a key stage in a complete proteomic experiment of tissues and cells, as it can s", "l 2. A schematic representation of the HaCaT proteomic research strategy is shown in Fig. 1. The po", ".Figure 1The experimental design used in the proteomic study of HaCaT keratinocytes. After growing"], "order_basis": "paper_text_order:1245", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["with detergents is frequently utilized with cultured mammalian cells. We used an SDS-containing b", "s. After growing to ~ 60–70% confluence, the cultured cells were divided into two groups, one was", "S is widely used for protein extraction from cultured cell lines26. Using the 2% SDS concentration", "lated expression induced by 17β-estradiol in MCF-7 breast cancer cells51. 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