High expression of GPNMB indicates an unfavorable prognosis in glioma: Combination of data from the GEO and CGGA databases and validation in tissue microarray.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32782553", "kind": "science-record", "revision": 8, "content_hash": "sha256:b3904623ef968d98bc7dc38fa011b229147cfe3bc23a0526a7d058aba8eeb3bf", "created_at": "2026-11-01T15:41:07Z", "updated_at": "2026-11-01T22:45:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "High expression of GPNMB indicates an unfavorable prognosis in glioma: Combination of data from the GEO and CGGA databases and validation in tissue microarray.", "doi": "10.3892/ol.2020.11787", "pmid": "32782553", "authors": ["Xiao Feng", "Lina Zhang", "Shanbao Ke", "Tao Liu", "Liuwei Hao", "Pan Zhao", "Wenzhi Tu", "Shundong Cang"], "journal": "Oncology letters", "year": 2020, "abstract": "Glycoprotein non-metastatic melanoma protein B (GPNMB), a transmembrane glycoprotein, has been reported to be involved in tumor progression, but its prognostic value for glioma and the mechanistic effects on glioma progression have not been clearly explored. The present study aimed to investigate the prognostic role of GPNMB in glioma and the potential mechanisms of how GPNMB mediates glioma progression. Differentially expressed genes between the four highest and four lowest GPNMB expression samples in the GSE53733 dataset were first determined. Gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis and Gene set enrichment analysis results demonstrated that the significantly enriched pathways in samples with high GPNMB expression compared with those with low GPNMB expression were associated with hypoxia, angiogenesis, migration and invasion. Pearson correlation analysis was conducted to investigate the correlations between GPNMB expression and the markers of hypoxia, angiogenesis, migration and invasion in GSE53733, which were further validated using another mRNA microarray dataset from the Chinese Glioma Genome Atlas (CGGA). In addition, using the CGGA dataset, high GPNMB expression was demonstrated to be significantly associated with advanced WHO grade and short survival time in patients with glioma. Of note, based on the immunohistochemical staining of the tissue microarrays, Kaplan-Meier analysis with the Renyi test and a Cox proportional hazards model were used to validate the unfavorable prognostic role of high GPNMB expression in glioma. In conclusion, high GPNMB expression may be associated with high tumor grade and unfavorable prognosis in glioma. GPNMB expression was demonstrated to correlate with the markers of hypoxia, angiogenesis, migration and invasion, which may be potential mechanisms through which GPNMB mediates glioma progression.", "claims": [{"id": "claim-method", "statement": "The DEGs between the top and bottom 4 GPNMB expression samples were identified using the limma package in R Project (29). The screening thresholds for DEGs were set at adjusted P-value=0.05 and log2 fold-change=2. Pearson correlation analysis was used for parametric tests; Spearman correlation analysis was used for non-parametric tests. The Kaplan-Meier method followed by log-rank test was used for survival analysis. The Renyi test was performed to detect differences when survival curves crossed over with the survMisc package in R. The Cox proportional hazards model was used for univariate and multivariate analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32782553", "locator": "sections[5] \"Screening differentially expressed genes (DEGs)\" paragraph 2", "quote": "The DEGs between the top and bottom 4 GPNMB expression samples were identified using the limma package in R Project (29)."}, {"asset": "source:pmid:32782553", "locator": "sections[5] \"Screening differentially expressed genes (DEGs)\" paragraph 2", "quote": "The screening thresholds for DEGs were set at adjusted P-value=0.05 and log2 fold-change=2."}, {"asset": "source:pmid:32782553", "locator": "sections[8] \"Correlation analysis\" paragraph 2", "quote": "Pearson correlation analysis was used for parametric tests; Spearman correlation analysis was used for non-parametric tests."}, {"asset": "source:pmid:32782553", "locator": "sections[14] \"Statistical analysis\" paragraph 2", "quote": "The Kaplan-Meier method followed by log-rank test was used for survival analysis."}, {"asset": "source:pmid:32782553", "locator": "sections[14] \"Statistical analysis\" paragraph 2", "quote": "The Renyi test was performed to detect differences when survival curves crossed over with the survMisc package in R."}, {"asset": "source:pmid:32782553", "locator": "sections[14] \"Statistical analysis\" paragraph 2", "quote": "The Cox proportional hazards model was used for univariate and multivariate analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed in the present study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32782553", "locator": "sections[27] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and/or analyzed in the present study are available from the corresponding author upon reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:32782553"], "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:GSE53733"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE53733"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32782553", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/ol.2020.11787", "sha256": "sha256:ff8d1f9986c9c6f05a40aacaecbf6f91830cd44805befa7a9a31081a024de493", "bytes": 31035, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/ol.2020.11787", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7400985", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE53733", "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=GSE53733", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53733", "version": null, "note": "The datasets used and/or analyzed in the present study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed in the present study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1299517", "GSM1299518", "GSM1299519", "GSM1299520", "GSM1299521", "GSM1299522", "GSM1299523", "GSM1299524", "GSM1299525", "GSM1299526", "GSM1299527", "GSM1299528", "GSM1299529", "GSM1299530", "GSM1299531", "GSM1299532", "GSM1299533", "GSM1299534", "GSM1299535", "GSM1299536", "GSM1299537", "GSM1299538", "GSM1299539", "GSM1299540", "GSM1299541", "GSM1299542", "GSM1299543", "GSM1299544", "GSM1299545", "GSM1299546", "GSM1299547", "GSM1299548", "GSM1299549", "GSM1299550", "GSM1299551", "GSM1299552", "GSM1299553", "GSM1299554", "GSM1299555", "GSM1299556", "GSM1299557", "GSM1299558", "GSM1299559", "GSM1299560", "GSM1299561", "GSM1299562", "GSM1299563", "GSM1299564", "GSM1299565", "GSM1299566", "GSM1299567", "GSM1299568", "GSM1299569", "GSM1299570", "GSM1299571", "GSM1299572", "GSM1299573", "GSM1299574", "GSM1299575", "GSM1299576", "GSM1299577", "GSM1299578", "GSM1299579", "GSM1299580", "GSM1299581", "GSM1299582", "GSM1299583", "GSM1299584", "GSM1299585", "GSM1299586"], "sample_count": 70, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from primary Glioblastoma in adults", "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:GSE53733 not downloaded", "asset:data:geo:GSE53733 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "reordered", "quote": "The DEGs between the top and bottom 4 GPNMB expression samples were identified using the limma package in R Project (29). 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Of note, based on the immunohistochemical staining of the tissue microarrays, Kaplan-M"], "order_basis": "paper_text_order:1490", "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": ["Materials and methods Cell culture and siRNA transfection U-87MG (U87) glioblastoma cell line of unkno", "e seeded in 6-well plates overnight and then transfected with 50 nM siRNA using Lipofectamine® 2000 (", "sequent experiments were conducted 24 h post-transfection. Statistical analysis Data are presented as", "Materials and methods Cell culture and siRNA transfection U-87MG (U87) glioblastoma cell"], "order_basis": "paper_text_order:2070", "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": ["Collection (cat. no. HTB-14). U87 cells were cultured in Dulbecco's modified Eagle's medium (Thermo F"], "order_basis": "paper_text_order:2226", "id": "assay:3"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["as the mean ± standard error of the mean. In CCK-8 assay, 6 independent repeats for each group"], "order_basis": "paper_text_order:2984", "id": "assay:4"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The DEGs between the top and bottom 4 GPNMB expression samples were identified using the limma package in R Project (29). The screening thresholds for DEGs were set at adjusted P-value=0.05 and log2 fold-change=2. Pearson correlation analysis was used for parametric tests; Spearman correlation analysis was used for non-parametric tests. The Kaplan-Meier method followed by log-rank test was used for survival analysis. The Renyi test was performed to detect differences when survival curves crossed over with the survMisc package in R. 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