Identification of allograft inflammatory factor-1 suppressing the progression and indicating good prognosis of osteosarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38521928", "kind": "science-record", "revision": 4, "content_hash": "sha256:7f77089b0c94d9aef66b7dfaca2aad5923cbbe69e28708e477c2e34378ab1b43", "created_at": "2026-11-01T19:20:28Z", "updated_at": "2026-11-01T22:53:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of allograft inflammatory factor-1 suppressing the progression and indicating good prognosis of osteosarcoma.", "doi": "10.1186/s12891-024-07363-8", "pmid": "38521928", "authors": ["Wenda Liu", "Tao Shi", "Di Zheng", "Guangshui Ke", "Jingteng Chen"], "journal": "BMC musculoskeletal disorders", "year": 2024, "abstract": "BACKGROUND: Osteosarcoma is one of the most common cancers worldwide. Intense efforts have been made to elucidate the pathogeny, but the mechanisms of osteosarcoma are still not well understood. We aimed to investigate the potential biomarker, allograft inflammatory factor-1 (AIF1), affecting the progression and prognosis of osteosarcoma.\nMETHODS: Three microarray datasets were downloaded from GEO datasets and one was obtained from the TCGA dataset. The differentially expressed genes (DEGs) were identified. GO and KEGG functional enrichment analyses of overlapped DEGs were performed. The PPI network of overlapped DEGs was constructed by STRING and visualized with Cytoscape. Overall survival (OS) and Metastasis free survival (MFS) were analyzed from GSE21257. Finally, the effect of the most relevant core gene affecting the progression of osteosarcoma was examined in vitro.\nRESULTS: One hundred twenty six DEGs were identified, consisting of 65 upregulated and 61 downregulated genes. Only AIF1 was significantly associated with OS and MFS. It was found that AIF1 could be enriched into the NF-κB signaling pathway. GSEA and ssGSEA analyses showed that AIF1 was associated with the immune invasion of tumors. Cell experiments showed that AIF1 was underexpressed in osteosarcoma cell lines, while the malignant propriety was attenuated after overexpressing the expression of AIF1. Moreover, AIF1 also affects the expression of the NF-κB pathway.\nCONCLUSION: In conclusion, DEGs and hub genes identified in the present study help us understand the molecular mechanisms underlying the carcinogenesis and progression of osteosarcoma, and provide candidate targets for diagnosis and treatment of osteosarcoma.", "claims": [{"id": "claim-method", "statement": "The assessment of the predictive value of the genes was conducted utilizing the log-rank test, which is also referred to as the Mantel-Cox test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38521928", "locator": "sections[8] \"Kaplan-Meier survival analysis\" paragraph 2", "quote": "The assessment of the predictive value of the genes was conducted utilizing the log-rank test, which is also referred to as the Mantel-Cox test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We obtained the datasets analyzed and generated during the current study in the TCGA GDC repository (https://portal.gdc.cancer.gov) and GEO repository (https://www.ncbi.nlm.nih.gov/geo/). All data included in this study are available upon request by contact with the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38521928", "locator": "sections[36] \"notes\" paragraph 1", "quote": "We obtained the datasets analyzed and generated during the current study in the TCGA GDC repository (https://portal.gdc.cancer.gov) and GEO repository (https://www.ncbi.nlm.nih.gov/geo/). All data included in this study are available upon request by contact with the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Only AIF1 was significantly associated with overall survival and metastasis-free survival.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38521928", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Only AIF1 was significantly associated with OS and MFS."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Only AIF1 was significantly associated with overall survival and metastasis-free survival.", "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:38521928"], "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:GSE21257"], "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:GSE21257"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38521928", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12891-024-07363-8", "sha256": "sha256:96e6defd01b4ad5a77f29dd1f2a20d0c3a1c7f79de8aa9405e0339e898b79cff", "bytes": 46210, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12891-024-07363-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10960474", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE21257", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21257", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE21257", "version": null, "note": "We obtained the datasets analyzed and generated during the current study in the TCGA GDC repository (https://portal.gdc.cancer.gov) and GEO repository (https://www.ncbi.nlm.nih.gov/geo/). 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All data included in this study are available upon request by contact with the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM530667", "GSM530899", "GSM531283", "GSM531284", "GSM531285", "GSM531286", "GSM531287", "GSM531288", "GSM531289", "GSM531290", "GSM531291", "GSM531292", "GSM531293", "GSM531294", "GSM531295", "GSM531296", "GSM531297", "GSM531298", "GSM531299", "GSM531300", "GSM531301", "GSM531302", "GSM531303", "GSM531304", "GSM531305", "GSM531306", "GSM531307", "GSM531308", "GSM531309", "GSM531310", "GSM531311", "GSM531312", "GSM531313", "GSM531314", "GSM531319", "GSM531320", "GSM531321", "GSM531322", "GSM531323", "GSM531324", "GSM531325", "GSM531326", "GSM531327", "GSM531328", "GSM531329", "GSM531330", "GSM531331", "GSM531332", "GSM531333", "GSM531334", "GSM531335", "GSM531351", "GSM531352"], "sample_count": 53, "group_sizes": null, "group_sizes_basis": null, "platform": "10295", "taxon": "Homo sapiens", "title": "Genome-wide gene expression profiling on pre-chemotherapy biopsies of osteosarcoma patients who developed metastases within 5yrs (n=34) and patients who did not develop metastases within 5yrs (n=19)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE21257 not downloaded", "asset:data:geo:GSE21257 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 assessment of the predictive value of the genes was conducted utilizing the log-rank test, which is also referred to as the Mantel-Cox test."}}, {"id": "method-2", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-4", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}], "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE21257"], "resolved_accessions": ["GSE21257"], "statements": ["We obtained the datasets analyzed and generated during the current study in the TCGA GDC repository (https://portal.gdc.cancer.gov) and GEO repository (https://www.ncbi.nlm.nih.gov/geo/). All data included in this study are available upon request by contact with the corresponding author."], "basis": "The paper names GSE21257 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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METHODS: Three microarray datasets were downloaded from GEO datasets a"], "order_basis": "paper_text_order:436", "id": "assay:1"}, {"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": ["and the expression of AIF1. Cell culture and transfection The 143B, MG63, HOS, and hFOB1.19 cell lines", "China) were employed to generate lentivirus transfection constructs to induce AIF1 overexpression (LV"], "order_basis": "paper_text_order:3843", "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": 0.77, "evidence": ["conduct the in vitro assays. 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