Identification of a Novel Gene ARNT2 for Osteogenic Differentiation of Mesenchymal Stem Cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40679635", "kind": "science-record", "revision": 4, "content_hash": "sha256:225767807fc06e8cdcd140bb0a0065e67cb1a4efdb4f7ef5efb29baf7371e731", "created_at": "2026-11-01T20:30:47Z", "updated_at": "2026-11-01T22:56:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a Novel Gene ARNT2 for Osteogenic Differentiation of Mesenchymal Stem Cells.", "doi": "10.1007/s00223-025-01407-4", "pmid": "40679635", "authors": ["Mina Ding", "Zhiwei Hu", "Ke Pei", "Junyuan Hu", "Yan Liao", "Cheguo Cai", "Jian V Zhang"], "journal": "Calcified tissue international", "year": 2025, "abstract": "The balance between adipogenesis and osteogenesis in mesenchymal stem cells (MSCs) is pivotal for the maintenance of bone homeostasis. However, the genes responsible for regulating this balance are still not fully understood. This investigation sought to explore and identify novel genes that influence MSC differentiation into adipogenic and osteogenic lineages, thereby enhancing bone formation. Four datasets from the Gene Expression Omnibus (GEO) database were utilized: three focused on osteogenic differentiation (GSE73087, GSE18043, GSE114117), and one on adipogenic differentiation (GSE37836). Differentially expressed genes (DEGs) during both osteogenic and adipogenic differentiation processes were analyzed using the limma R package. A sum of 471 common differentially expressed genes (CDEGs) were found in MSC osteogenesis, comprising 240 elevated and 231 reduced genes. Similarly, in MSCs adipogenesis, 204 elevated genes and 459 reduced genes were identified. Fourteen hub genes were found to overlap between the CDEGs associated with MSC osteogenesis and DEGs linked to adipogenic differentiation. Notably, the expression of aryl hydrocarbon receptor nuclear translocator 2 (ARNT2) was elevated during osteogenesis but reduced during adipogenesis. Overexpression of ARNT2 enhanced the expression of osteogenic markers in MSCs, while its suppression led to a decrease in osteogenic marker expression. Protein-protein interaction network analysis revealed that ARNT2 interacts with Hypoxia inducible factor 1 subunit alpha (HIF1A), B-cell lymphoma 6 (BCL6), Ubiquitin-specific-processing protease 7 (USP7), and Single-minded homolog 2 (SIM2), which are implicated in the regulation of MSCs osteogenesis. In summary, fourteen hub genes were identified as potential regulators in the osteo-adipogenic differentiation of MSCs. Among them, ARNT2 was confirmed to promote osteogenesis in MSCs and exhibited potential as a therapeutic target for bone-related diseases.", "claims": [{"id": "claim-method", "statement": "DEGs in the osteogenic and adipogenic differentiation of MSCs were identified using the Limma package (Version 3.54.2, RRID:SCR_010943) in R software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40679635", "locator": "sections[4] \"Identification of DEGs and Functional Enrichment Analysis of Hub Genes\" paragraph 2", "quote": "DEGs in the osteogenic and adipogenic differentiation of MSCs were identified using the Limma package (Version 3.54.2, RRID:SCR_010943) in R software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data used in this article are presented in the article and supplementary material. 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The cells were cultured in Nutristem MSC XF Basal Medium (Sartorius, Be"], "order_basis": "paper_text_order:3415", "id": "assay:1"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["e incubated at 37 °C in a 5% CO2 atmosphere. Flow cytometry was utilized to assess the expression of ste"], "order_basis": "paper_text_order:3740", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["performed following ARNT2 overexpression and knockdown. The results indicated that the mRNA levels", "overexpression (Fig. 8A). Conversely, ARNT2 knockdown resulted in a marked reduction in the mRNA e", "in UCMSCs. Effect of ARNT2 overexpression or knockdown on the potential target gene in UCMSCs. A Th", "luding HIF1A, BCL6, USP7, and SIM2, in ARNT2-knockdown UCMSCs and control UCMSCs was analyzed by qR"], "order_basis": "paper_text_order:11759", "id": "assay:3"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["DEGs in the osteogenic and adipogenic differentiation of MSCs were identified using the Limma package (Version 3.54.2, RRID:SCR_010943) in R software."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}