Comprehensive Bioinformatics Analysis Reveals the Potential Role of the hsa_circ_0001081/miR-26b-5p Axis in Regulating COL15A1 and TRIB3 within Hypoxia-Induced miRNA/mRNA Networks in Glioblastoma Cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39457549", "kind": "science-record", "revision": 3, "content_hash": "sha256:b28bc1b7e5534b78094d1a5c614079420e86d084a13a25a41ced1a4e449fb03f", "created_at": "2026-11-01T20:29:43Z", "updated_at": "2026-11-01T22:13:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive Bioinformatics Analysis Reveals the Potential Role of the hsa_circ_0001081/miR-26b-5p Axis in Regulating COL15A1 and TRIB3 within Hypoxia-Induced miRNA/mRNA Networks in Glioblastoma Cells.", "doi": "10.3390/biomedicines12102236", "pmid": "39457549", "authors": ["Bartosz Lenda", "Marta Żebrowska-Nawrocka", "Ewa Balcerczak"], "journal": "Biomedicines", "year": 2024, "abstract": "Background/Objectives: The intrinsic molecular heterogeneity of glioblastoma (GBM) is one of the main reasons for its resistance to conventional treatment. Mesenchymal GBM niches are associated with hypoxic signatures and a negative influence on patients' prognosis. To date, competing endogenous RNA (ceRNA) networks have been shown to have a broad impact on the progression of various cancers. In this study, we decided to construct hypoxia-specific microRNA/ messengerRNA (miRNA/mRNA) networks with a putative circular RNA (circRNA) regulatory component using available bioinformatics tools. Methods: For ceRNA network construction, we combined publicly available data deposited in the Gene Expression Omnibus (GEO) and interaction pairs obtained from miRTarBase and circBank; a differential expression analysis of GBM cells was performed with limma and deseq2. For the gene ontology (GO) enrichment analysis, we utilized clusterProfiler; GBM molecular subtype analysis was performed in the Glioma Bio Discovery Portal (Glioma-BioDP). Results: We observed that miR-26b-5p, generally considered a tumor suppressor, was upregulated under hypoxic conditions in U-87 MG cells. Moreover, miR-26b-5p could potentially inhibit TRIB3, a gene associated with tumor proliferation. Protein-protein interaction (PPI) network and GO enrichment analyses identified a hypoxia-specific subcluster enriched in collagen-associated terms, with six genes highly expressed in the mesenchymal glioma group. This subcluster included hsa_circ_0001081/miR-26b-5p-affected COL15A1, a gene downregulated in hypoxic U-87 MG cells yet highly expressed in the mesenchymal GBM subtype. Conclusions: The interplay between miR-26b-5p, COL15A1, and TRIB3 suggests a complex regulatory mechanism that may influence the extracellular matrix composition and the mesenchymal transformation in GBM. However, the precise impact of the hsa_circ_0001081/miR-26b-5p axis on collagen-associated processes in hypoxia-induced GBM cells remains unclear and warrants further investigation.", "claims": [{"id": "claim-method", "statement": "Differences in expression levels of the examined genes between pairs of each subtype were compared by t-test; we assumed that a p < 0.05 means that the difference is statistically significant. For survival analysis, we obtained data from the TCGA-GBM cohort deposited in the GDC Data Portal (https://portal.gdc.cancer.gov/, accessed on 19 June 2024) using the TCGAbiolinks package. A Kaplan–Meier analysis and log-rank test were conducted using the survminer and survival packages. We assumed that a log-rank p < 0.05 was statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39457549", "locator": "sections[6] \"2.4. 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These data were derived from the following resources available in the public domain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245800 [accessed on 16 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142719 [accessed on 8 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146463 [accessed on 23 June 2024]; The original data presented in the study are openly available in Zenodo at DOI 10.5281/zenodo.13770443.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39457549", "locator": "sections[18] \"notes\" paragraph 1", "quote": "The data presented in this study are available in the Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, [accessed on 13 August 2024], reference numbers GSE245800, GSE142719, and GSE146463. These data were derived from the following resources available in the public domain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245800 [accessed on 16 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142719 [accessed on 8 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146463 [accessed on 23 June 2024]; The original data presented in the study are openly available in Zenodo at DOI 10.5281/zenodo.13770443."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:39457549"], "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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These data were derived from the following resources available in the public domain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245800 [accessed on 16 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142719 [accessed on 8 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146463 [accessed on 23 June 2024]; The original data presented in the study are openly available in Zenodo at DOI 10.5281/zenodo.13770443.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this study are available in the Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, [accessed on 13 August 2024], reference numbers GSE245800, GSE142719, and GSE146463. These data were derived from the following resources available in the public domain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245800 [accessed on 16 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142719 [accessed on 8 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146463 [accessed on 23 June 2024]; The original data presented in the study are openly available in Zenodo at DOI 10.5281/zenodo.13770443.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4386266", "GSM4386267", "GSM4386268", "GSM4386269", "GSM4386270", "GSM4386271", "GSM4386272", "GSM4386273", "GSM4386274", "GSM4386275", "GSM4386276"], "sample_count": 11, "group_sizes": null, "group_sizes_basis": null, "platform": "21825", "taxon": "Homo sapiens", "title": "Development of circRNA expression signatures for glioblastoma cells.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE245800", "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=GSE245800", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE245800", "version": null, "note": "The data presented in this study are available in the Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, [accessed on 13 August 2024], reference numbers GSE245800, GSE142719, and GSE146463. 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These data were derived from the following resources available in the public domain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245800 [accessed on 16 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142719 [accessed on 8 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146463 [accessed on 23 June 2024]; The original data presented in the study are openly available in Zenodo at DOI 10.5281/zenodo.13770443.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM7849243", "GSM7849244", "GSM7849245", "GSM7849246", "GSM7849247", "GSM7849248"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Proteotranscriptomic decoding of the surface-endocytome in primary glioblastoma cells identifies potential target antigens in the hypoxic tumor niche [U87_mRNA_Norm_Hyp]", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE142719 not downloaded", "asset:data:geo:GSE142719 licence not read", "asset:data:geo:GSE146463 not downloaded", "asset:data:geo:GSE146463 licence not read", "asset:data:geo:GSE245800 not downloaded", "asset:data:geo:GSE245800 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "Differences in expression levels of the examined genes between pairs of each subtype were compared by t-test; we assumed that a p < 0.05 means that the difference is statistically significant. 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