Prognostic impact of a lymphocyte activation-associated gene signature in GBM based on transcriptome analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34527446", "kind": "science-record", "revision": 7, "content_hash": "sha256:3707a15828c8896794eeb7154c42c9d29a0abf0dd6eb7b1ef2f0eb0f162d5a80", "created_at": "2026-11-01T15:41:52Z", "updated_at": "2026-11-01T22:04:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic impact of a lymphocyte activation-associated gene signature in GBM based on transcriptome analysis.", "doi": "10.7717/peerj.12070", "pmid": "34527446", "authors": ["Yujia Lan", "Erjie Zhao", "Xinxin Zhang", "Xiaojing Zhu", "Linyun Wan", "Suru A", "Yanyan Ping", "Yihan Wang"], "journal": "PeerJ", "year": 2021, "abstract": "BACKGROUND: Glioblastoma multiforme (GBM) is a highly, malignant tumor of the primary central nervous system. Patients diagnosed with this type of tumor have a poor prognosis. Lymphocyte activation plays important roles in the development of cancers and its therapeutic treatments.\nOBJECTIVE: We sought to identify an efficient lymphocyte activation-associated gene signature that could predict the progression and prognosis of GBM.\nMETHODS: We used univariate Cox proportional hazards regression and stepwise regression algorithm to develop a lymphocyte activation-associated gene signature in the training dataset (TCGA, n = 525). Then, the signature was validated in two datasets, including GSE16011 (n = 150) and GSE13041 (n = 191) using the Kaplan Meier method. Univariate and multivariate Cox proportional hazards regression models were used to adjust for clinicopathological factors.\nRESULTS: We identified a lymphocyte activation-associated gene signature (TCF3, IGFBP2, TYRO3 and NOD2) in the training dataset and classified the patients into high-risk and low-risk groups with significant differences in overall survival (median survival 15.33 months vs 12.57 months, HR = 1.55, 95% CI [1.28-1.87], log-rank test P < 0.001). This signature showed similar prognostic values in the other two datasets. Further, univariate and multivariate Cox proportional hazards regression models analysis indicated that the signature was an independent prognostic factor for GBM patients. Moreover, we determined that there were differences in lymphocyte activity between the high- and low-risk groups of GBM patients among all datasets. Furthermore, the lymphocyte activation-associated gene signature could significantly predict the survival of patients with certain features, including IDH-wildtype patients and patients undergoing radiotherapy. In addition, the signature may also improve the prognostic power of age.\nCONCLUSIONS: In summary, our results suggested that the lymphocyte activation-associated gene signature is a promising factor for the survival of patients, which is helpful for the prognosis of GBM patients.", "claims": [{"id": "claim-method", "statement": "The survival differences between the two groups were visualized by Kaplan–Meier analysis and were compared by the log-rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34527446", "locator": "sections[5] \"Statistical analysis\" paragraph 2", "quote": "The survival differences between the two groups were visualized by Kaplan–Meier analysis and were compared by the log-rank test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nThe data are available at TCGA (TCGA-GBM) and NCBI GEO (GSE16011 and GSE13041).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34527446", "locator": "sections[25] \"Data Availability Statement\" paragraphs 1-3", "quote": "The following information was supplied regarding data availability:\nThe data are available at TCGA (TCGA-GBM) and NCBI GEO (GSE16011 and GSE13041)."}], "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:34527446"], "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:GSE13041"], "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:group_comparison_wilcoxon", "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:GSE13041"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34527446", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.12070", "sha256": "sha256:1d34359908a85b09d698c2af9c6858e55d0af861a5ab5773b9dddf28c6a64545", "bytes": 41027, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.12070", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8401751", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13041", "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=GSE13041", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13041", "version": null, "note": "The following information was supplied regarding data availability:\nThe data are available 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