Three Immune-Associated Subtypes of Diffuse Glioma Differ in Immune Infiltration, Immune Checkpoint Molecules, and Prognosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33425739", "kind": "science-record", "revision": 7, "content_hash": "sha256:3e5beb0fd8ba04a35ee1cf34c8b5d8c34d4a3289ec2de503ca43ebefafa5e02d", "created_at": "2026-11-01T15:41:22Z", "updated_at": "2026-11-01T22:02:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Three Immune-Associated Subtypes of Diffuse Glioma Differ in Immune Infiltration, Immune Checkpoint Molecules, and Prognosis.", "doi": "10.3389/fonc.2020.586019", "pmid": "33425739", "authors": ["Quanwei Zhou", "Xuejun Yan", "Weidong Liu", "Wen Yin", "Hongjuan Xu", "Damei Cheng", "Xingjun Jiang", "Caiping Ren"], "journal": "Frontiers in oncology", "year": 2020, "abstract": "Diffuse glioma is one of the most prevalent malignancies of the brain, with high heterogeneity of tumor-infiltrating immune cells. However, immune-associated subtypes of diffuse glioma have not been determined, nor has the effect of different immune-associated subtypes on disease prognosis and immune infiltration of diffuse glioma patients. We retrieved the expression profiles of immune-related genes from The Cancer Genome Atlas (TCGA) (n = 672) and GSE16011 (n = 268) cohorts and used them to identify subtypes of diffuse glioma via Consensus Cluster Plus analysis. We used the limma, clusterProfiler, ESTIMATE, and survival packages of R for differential analysis, functional enrichment, immune and stromal score evaluation respectively in three subtypes, and performed log-rank tests in immune subtypes of diffuse glioma. The immune-associated features of diffuse glioma in the two cohorts were characterized via bioinformatic analyses of the mRNA expression data of immune-related genes. Three subtypes (C1-3) of diffuse glioma were identified from TCGA data, and were verified using the GSE16011 cohort. We then evaluated their immune characteristics and clinical features. Our mRNA profiling analyses indicated that the different subtypes of diffuse glioma presented differential expression profile of specific genes and signal pathways in the TCGA cohort. Patients with subtype C1, who were mostly diagnosed with grade IV glioma, had poorer outcomes than patients with subtype C2 or C3. Subtype C1 was characterized by a higher degree of immune cell infiltration as estimated by GSVA, and more frequent wildtype IDH1. By contrast, subtype C3 included more grade II and IDH1-mutated glioma, and was associated with more infiltration of CD4+T cells. Most subtype C2 had the features between subtypes C1 and C3. Meanwhile, immune checkpoints and their ligand molecules, including PD1/(PD-L1/PDL2), CTLA4/(CD80/CD86), and B7H3/TLT2, were significantly upregulated in subtype C1 and downregulated in subtype C3. In addition, patients with subtype C1 exhibited more frequent gene mutations. Univariate and multivariate Cox regression analyses revealed that diffuse glioma subtype was an effective, independent, and better prognostic factor. Therefore, we established a novel immune-related classification of diffuse glioma, which provides potential immunotherapy targets for diffuse glioma.", "claims": [{"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material , further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33425739", "locator": "sections[18] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material , further inquiries can be directed to the corresponding authors."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:33425739"], "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:GSE16011"], "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:GSE16011"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33425739", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2020.586019", "sha256": "sha256:583aea706b14df2181452a9b1c6147b8144d883590d79dd7ea99051d4547858f", "bytes": 41067, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2020.586019", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7786360", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16011", "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=GSE16011", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16011", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material , further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material , further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM405200", "GSM405201", "GSM405202", "GSM405203", "GSM405204", "GSM405205", "GSM405206", "GSM405207", "GSM405208", "GSM405209", "GSM405210", "GSM405211", "GSM405212", "GSM405213", "GSM405214", "GSM405215", "GSM405216", "GSM405217", "GSM405218", "GSM405219", "GSM405220", "GSM405221", "GSM405222", "GSM405223", "GSM405224", "GSM405225", "GSM405226", "GSM405227", "GSM405228", "GSM405229", "GSM405230", "GSM405231", "GSM405232", "GSM405233", "GSM405234", "GSM405235", "GSM405236", "GSM405237", "GSM405238", "GSM405239", "GSM405240", "GSM405241", "GSM405242", "GSM405243", "GSM405244", "GSM405245", "GSM405246", "GSM405247", "GSM405248", "GSM405249", "GSM405250", "GSM405251", "GSM405252", "GSM405253", "GSM405254", "GSM405255", "GSM405256", "GSM405257", "GSM405258", "GSM405259", "GSM405260", "GSM405261", "GSM405262", "GSM405263", "GSM405264", "GSM405265", "GSM405266", "GSM405267", "GSM405268", "GSM405269", "GSM405270", "GSM405271", "GSM405272", "GSM405273", "GSM405274", "GSM405275", "GSM405276", "GSM405277", "GSM405278", "GSM405279", "GSM405280", "GSM405281", "GSM405282", "GSM405283", "GSM405284", "GSM405285", "GSM405286", "GSM405287", "GSM405288", "GSM405289", "GSM405290", "GSM405291", "GSM405292", "GSM405293", "GSM405294", "GSM405295", "GSM405296", "GSM405297", "GSM405298", "GSM405299", "GSM405300", "GSM405301", "GSM405302", "GSM405303", "GSM405304", "GSM405305", "GSM405306", "GSM405307", "GSM405308", "GSM405309", "GSM405310", "GSM405311", "GSM405312", "GSM405313", "GSM405314", "GSM405315", "GSM405316", "GSM405317", "GSM405318", "GSM405319", "GSM405320", "GSM405321", "GSM405322", "GSM405323", "GSM405324", "GSM405325", "GSM405326", "GSM405327", "GSM405328", "GSM405329", "GSM405330", "GSM405331", "GSM405332", "GSM405333", "GSM405334", "GSM405335", "GSM405336", "GSM405337", "GSM405338", "GSM405339", "GSM405340", "GSM405341", "GSM405342", "GSM405343", "GSM405344", "GSM405345", "GSM405346", "GSM405347", "GSM405348", "GSM405349", "GSM405350", "GSM405351", "GSM405352", "GSM405353", "GSM405354", "GSM405355", "GSM405356", "GSM405357", "GSM405358", "GSM405359", "GSM405360", "GSM405361", "GSM405362", "GSM405363", "GSM405364", "GSM405365", "GSM405366", "GSM405367", "GSM405368", "GSM405369", "GSM405370", "GSM405371", "GSM405372", "GSM405373", "GSM405374", "GSM405375", "GSM405376", "GSM405377", "GSM405378", "GSM405379", "GSM405380", "GSM405381", "GSM405382", "GSM405383", "GSM405384", "GSM405385", "GSM405386", "GSM405387", "GSM405388", "GSM405389", "GSM405390", "GSM405391", "GSM405392", "GSM405393", "GSM405394", "GSM405395", "GSM405396", "GSM405397", "GSM405398", "GSM405399", "GSM405400", "GSM405401", "GSM405402", "GSM405403", "GSM405404", "GSM405405", "GSM405406", "GSM405407", "GSM405408", "GSM405409", "GSM405410", "GSM405411", "GSM405412", "GSM405413", "GSM405414", "GSM405415", "GSM405416", "GSM405417", "GSM405418", "GSM405419", "GSM405420", "GSM405421", "GSM405422", "GSM405423", "GSM405424", "GSM405425", "GSM405426", "GSM405427", "GSM405428", "GSM405429", "GSM405430", "GSM405431", "GSM405432", "GSM405433", "GSM405434", "GSM405435", "GSM405436", "GSM405437", "GSM405438", "GSM405439", "GSM405440", "GSM405441", "GSM405442", "GSM405443", "GSM405444", "GSM405445", "GSM405446", "GSM405447", "GSM405448", "GSM405449", "GSM405450", "GSM405451", "GSM405452", "GSM405453", "GSM405454", "GSM405455", "GSM405456", "GSM405457", "GSM405458", "GSM405459", "GSM405460", "GSM405461", "GSM405462", "GSM405463", "GSM405464", "GSM405465", "GSM405466", "GSM405467", "GSM405468", "GSM405469", "GSM405470", "GSM405471", "GSM405472", "GSM405473", "GSM405474", "GSM405475", "GSM405476", "GSM405477", "GSM405478", "GSM405479", "GSM405480", "GSM405481", "GSM405482", "GSM405483"], "sample_count": 284, "group_sizes": null, "group_sizes_basis": null, "platform": "8542", "taxon": "Homo sapiens", "title": "Intrinsic Gene Expression Profiles of Gliomas are a Better Predictor of Survival than Histology", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33425739:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:264b80ddc6e3501e98052ad92f901d53190f2158d54b95a710ba93f4c01ebb63", "bytes": 1793, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T1", "version": null, "note": "Association of the three immune-related with clinical characteristics in TCGA cohort.", "structure": {"pmcid": "PMC7786360", "section_index": 12, "section_title": "Characteristics of the Three Subtypes of Diffuse Glioma", "row_count": 33, "column_count": 6}, "table": {"label": "Table 1", "caption": "Association of the three immune-related with clinical characteristics in TCGA cohort.", "rows": [["Clinical Characteristics", "", "Molecular subtypes (n, %)", "p value"], ["", "C1(97,14.4)", "C2(397,59.1)", "C3(178,26.5)", ""], ["Age", "", "", "", "", "< 0.0001"], ["", "<40y", "14(14.4)", "139(35.0)", "71(40.0)", ""], ["", ">=40y", "82(84.5)", "215(54.2)", "92(51.7)", ""], ["", "N/A", "1(1.0)", "43(10.8)", "15(8.4)", ""], ["Gender", "", "", "", "", "0.012"], ["", "Female", "32(33.0)", "151(38.0)", "71(40.0)", ""], ["", "Male", "64(66.0)", "203(51.1)", "91(51.1)", ""], ["", "N/A", "1(1.0)", "43(10.8)", "15(8.4)", ""], ["Histology", "", "", "", "", "< 0.0001"], ["", "Astrocytoma", "5(5.2)", "128(32.2)", "34(19.1)", ""], ["", "Oligodendroglioma", "5(5.2)", "87(21.9)", "82(46.1)", ""], ["", "Oligoastrocytoma", "2(2.1)", "81(20.4)", "29(16.3)", ""], ["", "Glioblastoma", "84(86.6)", "58(14.6)", "18(10.1)", ""], ["", "N/A", "1(1.0)", "43(10.8)", "15(8.4)", ""], ["Grade", "", "", "", "", "< 0.0001"], ["", "G2", "1(1.0)", "143(36.0)", "72(40.4)", ""], ["", "G3", "11(11.3)", "153(38.5)", "73(41.0)", ""], ["", "G4", "84(86.6)", "58(14.6)", "18(10.1)", ""], ["", "N/A", "1(1.0)", "43(10.8)", "15(8.4)", ""], ["IDH status", "", "", "", "", "< 0.0001"], ["", "Mutant", "80(82.5)", "115(29.0)", "43(24.2)", ""], ["", "WT", "11(11.3)", "279(70.3)", "135(75.8)", ""], ["", "N/A", "6(6.2)", "3(0.8)", "0(0)", ""], ["1p/19q codeletion", "", "", "", "", "< 0.0001"], ["", "Non-codel", "2(2.1)", "89(22.4)", "77(43.3)", ""], ["", "Codel", "93(95.8)", "304(76.6)", "101(56.7)", ""], ["", "N/A", "2(2.1)", "4(1.0)", "0(0)", ""], ["MGMT promoter status", "", "", "", "", "< 0.0001"], ["", "Unmethylated", "44(45.3)", "93(23.4)", "27(15.2)", ""], ["", "Methylated", "32(33.0)", "296(74.6)", "146(82.0)", ""], ["", "N/A", "21(21.6)", "8(2.0)", "5(2.8)", ""]], "row_count": 33, "column_count": 6, "numeric_cells": 85, "header_rows": 2, "locator": "section[12]/table-wrap[1]#T1"}}], "gaps": ["asset:data:geo:GSE16011 not downloaded", "asset:data:geo:GSE16011 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Cox regression"}}, {"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": 0.7, "band": "medium", "quote": "log-rank"}}, {"id": "method-3", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-4", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "χ2"}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE16011"], "resolved_accessions": ["GSE16011"], "statements": ["The original contributions presented in the study are included in the article/ Supplementary Material , further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE16011 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:33425739", "data:geo:GSE16011", "asset:table:pmid:33425739:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE16011"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:21:36Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28116, "completion_tokens": 1839, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33425739", "type": "paper", "label": "pmid:33425739"}, {"id": "source:pmid:33425739", "type": "manuscript", "label": "PMID 33425739 full text"}, {"id": "data:geo:GSE16011", "type": "dataset", "label": "GEO GSE16011"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33425739", "type": "paper", "label": "pmid:33425739"}, {"id": "source:pmid:33425739", "type": "manuscript", "label": "PMID 33425739 full text"}, {"id": "data:geo:GSE16011", "type": "dataset", "label": "GEO GSE16011"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33425739", "type": "extraction", "used": ["source:pmid:33425739"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE16011", "type": "accession_resolution", "used": ["data:geo:GSE16011"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33425739", "parent_hash": "sha256:e602f7f8b53c1624bb55929020bff72ae5efb16acc24d86994047847049242b8", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE16011 licence not read", "asset:data:geo:GSE16011 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["a Processing High-throughput RNA sequencing (RNA-seq) data (n = 703), information on somatic muta", "A (https://tcga-data.nci.nih.gov/tcga/). Two RNA-seq datasets, TCGA-lower grade glioma (LGG) and", "Sources and Data Processing High-throughput RNA sequencing (RNA-seq) data (n = 703), information on som"], "order_basis": "paper_text_order:2549", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Cox regression"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}