ARHGEF3 Associated with Invasion, Metastasis, and Proliferation in Human Osteosarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34350290", "kind": "science-record", "revision": 6, "content_hash": "sha256:dfa64763271b2e95700db39d911d94cb56ae7f09f246853b96975cb067c07d49", "created_at": "2026-11-01T15:41:47Z", "updated_at": "2026-11-01T21:25:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "ARHGEF3 Associated with Invasion, Metastasis, and Proliferation in Human Osteosarcoma.", "doi": "10.1155/2021/3381957", "pmid": "34350290", "authors": ["Jie Gong", "Wei Tang", "Bin Lv", "Shushu Zhang", "Tingjuan Fan", "Guangyu Gao", "Dong Chen", "Yulong Liu"], "journal": "BioMed research international", "year": 2021, "abstract": "BACKGROUND: Osteosarcoma is a malignant bone tumor composed of mesenchymal cells producing osteoid and immature bone. This study is aimed at developing novel potential prognostic biomarkers and constructing a miRNA-mRNA network for progression in osteosarcoma.\nMETHOD: GSE70367 and GSE70414 were obtained in the Gene Expression Omnibus (GEO) database. GEO software and the GEO2R calculation method were used to analyze two gene profiles. The coexpression of differentially expressed miRNAs (DEMs) and genes (DEGs) was identified and searched for in the FunRich database for pathway and ontology analysis. Cytoscape was utilized to construct the mRNA-miRNA network. Survival analysis of identified miRNAs and mRNAs was performed by utilizing the Kaplan-Meier Plotter. Besides, expression levels of DEMs and target mRNAs were verified by performing quantitative real-time PCR (qRT-PCR) and Western blot (WB).\nRESULTS: Six differentially expressed microRNAs (DEMs) were identified, and 8 target genes were selected after screening. By using the KM Plotter software, miRNA-124 and ARHGEF3 were obviously associated with the overall survival of patients with osteosarcoma. Furthermore, ARHGEF3 was found downregulated in osteosarcoma cells by performing qRT-PCR and WB experiments. Results also showed that downregulated ARHGEF3 may associate with invasion, metastasis, and proliferation.\nCONCLUSIONS: By using microarray and bioinformatics analysis, DEMs were selected, and a complete miRNA-mRNA network was constructed. ARHGEF3 may act as a therapeutic and prognostic target of osteosarcoma.", "claims": [{"id": "claim-method", "statement": "The overall survival of OS patients was analyzed by the KM Plotter database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34350290", "locator": "sections[7] \"2.5. Analysis of the MicroRNAs and their Association with Osteosarcoma Prognosis\" paragraph 2", "quote": "The overall survival of OS patients was analyzed by the KM Plotter database."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34350290", "locator": "sections[24] \"Data Availability\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "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:34350290"], "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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Quantitative Real-Time PCR", "row_count": 3, "column_count": 3}, "table": {"label": "Table 1", "caption": "The primers for quantitative real-time polymerase chain reaction with GAPDH used as the internal standard control.", "rows": [["", "Forward", "Reverse"], ["ARHGEF3", "5′-GCCAGGATCGATATGGTTGCGAAGGACTAC-3′", "5′-AAGCTAGAATTCGCTCTCTCACAGGGCTGAC-3′"], ["GAPDH", "5′-TGGTATCGTGGAAGGACTCATGAC-3", "5′-ATGCCAGTGAGCTTCCCGTTCAGC-3"]], "row_count": 3, "column_count": 3, "numeric_cells": 4, "header_rows": 1, "locator": "section[9]/table-wrap[1]#tab1"}}], "gaps": ["asset:data:geo:GSE70367 not downloaded", "asset:data:geo:GSE70367 licence not read", "asset:data:geo:GSE70414 not downloaded", "asset:data:geo:GSE70414 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The overall survival of OS patients was analyzed by the KM Plotter database."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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RESULTS: Si"], "order_basis": "paper_text_order:902", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ing quantitative real-time PCR (qRT-PCR) and Western blot (WB). RESULTS: Six differentially expressed"], "order_basis": "paper_text_order:930", "id": "assay:2"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["is, and proliferation. CONCLUSIONS: By using microarray and bioinformatics analysis, DEMs were selec"], "order_basis": "paper_text_order:1448", "id": "assay:3"}, {"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": [". Osteosarcoma cells and hFOB1.19 cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Th", "ibodies The human OS cell lines (MG63, 143B, U2OS, U2R) were offered by Professor Kang Tie Ban"], "order_basis": "paper_text_order:2366", "id": "assay:4"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The overall survival of OS patients was analyzed by the KM Plotter database."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}