Comprehensive Analysis Reveals Prognostic and Therapeutic Immunity-Related Biomarkers for Pediatric Metastatic Osteosarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38256356", "kind": "science-record", "revision": 4, "content_hash": "sha256:dda710f5cff787fdcf68eb587ef7c5e2949836621e67d8995624d592a7933825", "created_at": "2026-11-01T19:20:10Z", "updated_at": "2026-11-01T22:53:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive Analysis Reveals Prognostic and Therapeutic Immunity-Related Biomarkers for Pediatric Metastatic Osteosarcoma.", "doi": "10.3390/medicina60010095", "pmid": "38256356", "authors": ["Jin Yuan", "Shengji Yu"], "journal": "Medicina (Kaunas, Lithuania)", "year": 2024, "abstract": "Background and Objectives: Osteosarcoma, the most prevalent malignant bone tumor in children and adolescents, presents a complex pathogenesis characterized by various genetic and epigenetic alterations. This study aims to identify key differentially expressed genes (DEGs) in pediatric osteosarcoma, with a focus on those influencing metastasis and patient survival. Materials and Methods: We utilized the GSE33382 dataset from the GEO database for a comprehensive bioinformatic analysis. This included a protein-protein interaction (PPI) network analysis, Cox regression, and Kaplan-Meier survival analysis to identify central DEGs associated with osteosarcoma metastasis and patient survival. Results: Our analysis identified 88 DEGs related to osteosarcoma metastasis. Among them, three survival-related central DEGs-C1QA, CD74, and HLA-DMA-were significantly linked to patient outcomes. Further correlation analysis established a strong relationship between these genes, tumor mutation burden (TMB), immune checkpoint gene expression, and overall survival. Notably, C1QA and CD74 exhibited higher expression in non-metastatic osteosarcoma cases, suggesting a potential role in disease progression. Conclusions: The identified DEGs, particularly C1QA, CD74, and HLA-DMA, may serve as critical biomarkers for pediatric osteosarcoma prognosis and potential targets for immunotherapy. These findings provide a deeper understanding of the molecular landscape of osteosarcoma and open new avenues for therapeutic intervention.", "claims": [{"id": "claim-method", "statement": "A Kaplan–Meier (KM) survival analysis with the log-rank test was also used to compare the survival difference between the above two groups. For Kaplan–Meier curves, p-values and hazard ratios (HRs) with 95% confidence intervals were generated by log-rank tests and univariate Cox proportional hazards regression with the R package (survival and survminer).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38256356", "locator": "sections[5] \"2.3. Survival-Related DEG Screening\" paragraph 2", "quote": "A Kaplan–Meier (KM) survival analysis with the log-rank test was also used to compare the survival difference between the above two groups. For Kaplan–Meier curves, p-values and hazard ratios (HRs) with 95% confidence intervals were generated by log-rank tests and univariate Cox proportional hazards regression with the R package (survival and survminer)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed for this study are available in publicly accessible repositories. The GSE33382 dataset was obtained from the GEO database. The TARGET-osteosarcoma dataset and GEPIA database were also utilized. These datasets were used under the open access guidelines provided by each database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38256356", "locator": "sections[18] \"Data Availability Statement\" paragraph 2", "quote": "The datasets analyzed for this study are available in publicly accessible repositories. The GSE33382 dataset was obtained from the GEO database. The TARGET-osteosarcoma dataset and GEPIA database were also utilized. These datasets were used under the open access guidelines provided by each database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified C1QA, CD74, and HLA-DMA as survival-related central DEGs significantly linked to patient outcomes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38256356", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our analysis identified 88 DEGs related to osteosarcoma metastasis. Among them, three survival-related central DEGs—C1QA, CD74, and HLA-DMA—were significantly linked to patient outcomes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified C1QA, CD74, and HLA-DMA as survival-related central DEGs significantly linked to patient outcomes.", "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:38256356"], "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:GSE33382"], "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:GSE33382"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38256356", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/medicina60010095", "sha256": "sha256:c56468637f20955cd0c4d49b10bac0755debefa1cec2f40483dd3d8db6c227b1", "bytes": 39881, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/medicina60010095", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10820594", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE33382", "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=GSE33382", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE33382", "version": null, "note": "The datasets analyzed for this study are available in publicly accessible repositories. 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