Dynamic proteomic profiling of human periodontal ligament stem cells during osteogenic differentiation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33536073", "kind": "science-record", "revision": 7, "content_hash": "sha256:a65208f82431cb734533af0d145dab4557bc9f1a6a0eb641abc48848baf50a9c", "created_at": "2026-11-01T15:41:24Z", "updated_at": "2026-11-01T22:03:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dynamic proteomic profiling of human periodontal ligament stem cells during osteogenic differentiation.", "doi": "10.1186/s13287-020-02123-6", "pmid": "33536073", "authors": ["Jianjia Li", "Zhifa Wang", "Xiangyu Huang", "Zhaodan Wang", "Zehao Chen", "Runting Wang", "Zhao Chen", "Wei Liu", "Buling Wu", "Fuchun Fang", "Wei Qiu"], "journal": "Stem cell research & therapy", "year": 2021, "abstract": "BACKGROUND: Human periodontal ligament stem cells (hPDLSCs) are ideal seed cells for periodontal regeneration. A greater understanding of the dynamic protein profiles during osteogenic differentiation contributed to the improvement of periodontal regeneration tissue engineering.\nMETHODS: Tandem Mass Tag quantitative proteomics was utilized to reveal the temporal protein expression pattern during osteogenic differentiation of hPDLSCs on days 0, 3, 7 and 14. Differentially expressed proteins (DEPs) were clustered and functional annotated by Gene Ontology (GO) terms. Pathway enrichment analysis was performed based on the Kyoto Encyclopedia of Genes and Genomes database, followed by the predicted activation using Ingenuity Pathway Analysis software. Interaction networks of redox-sensitive signalling pathways and oxidative phosphorylation (OXPHOS) were conducted and the hub protein SOD2 was validated with western blotting.\nRESULTS: A total of 1024 DEPs were identified and clustered in 5 distinctive clusters representing dynamic tendencies. The GO enrichment results indicated that proteins with different tendencies show different functions. Pathway enrichment analysis found that OXPHOS was significantly involved, which further predicted continuous activation. Redox-sensitive signalling pathways with dynamic activation status showed associations with OXPHOS to various degrees, especially the sirtuin signalling pathway. SOD2, an important component of the sirtuin pathway, displays a persistent increase during osteogenesis. Data are available via ProteomeXchange with identifier PXD020908.\nCONCLUSION: This is the first in-depth dynamic proteomic analysis of osteogenic differentiation of hPDLSCs. It demonstrated a dynamic regulatory mechanism of hPDLSC osteogenesis and might provide a new perspective for research on periodontal regeneration.", "claims": [{"id": "claim-data-access", "statement": "All data generated or analysed during this study are included in this published article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33536073", "locator": "sections[22] \"Availability of data and materials\" paragraph 2", "quote": "All data generated or analysed during this study are included in this published article."}], "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:33536073"], "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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"section[9]/table-wrap[1]#Tab1", "version": null, "note": "Osteogenesis-related proteins with differential expressions in the TMT proteomics", "structure": {"pmcid": "PMC7860046", "section_index": 9, "section_title": "Summary of TMT proteomics analysis", "row_count": 32, "column_count": 5}, "table": {"label": "Table 1", "caption": "Osteogenesis-related proteins with differential expressions in the TMT proteomics", "rows": [["Uniprot ID", "Protein name", "Gene name", "Clustera", "Reference"], ["Q12802", "A-kinase anchor protein 13", "AKAP13", "1", "[18]"], ["P07355", "Annexin A2", "ANXA2", "1", "[19]"], ["P35556", "Fibrillin-2", "FBN2", "1", "[20]"], ["Q04771", "Activin receptor type-1", "ACVR1", "2", "[21]"], ["P02765", "Alpha-2-HS-glycoprotein", "AHSG", "2", "[22]"], ["O00622", "CCN family member 1", "CCN1", "2", "[23]"], ["P02452", "Collagen alpha-1(I) chain", "COL1A1", "2", "[24]"], ["P08123", "Collagen alpha-2(I) chain", "COL1A2", "2", "[24]"], ["P02461", "Collagen alpha-1(III) 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"4", "[41]"], ["A1X283", "SH3 and PX domain-containing protein 2B", "SH3PXD2B", "4", "[42]"], ["P05186", "Alkaline phosphatase, tissue-nonspecific isozyme", "ALPL", "5", "Not list out"], ["P12109", "Collagen alpha-1(VI) chain", "COL6A1", "5", "[43]"], ["P35555", "Fibrillin-1", "FBN1", "5", "[44]"], ["Q13491", "Neuronal membrane glycoprotein M6-b", "GPM6B", "5", "[45]"], ["P52926", "High mobility group protein HMGI-C", "HMGA2", "5", "[46]"]], "row_count": 32, "column_count": 5, "numeric_cells": 117, "header_rows": 1, "locator": "section[9]/table-wrap[1]#Tab1"}}], "gaps": ["asset:data:geo:PXD020908 not downloaded", "asset:data:geo:PXD020908 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": 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