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pmid:34938284
TNFRSF11B Suppresses Memory CD4+ T Cell Infiltration in the Colon Cancer Microenvironment: A Multiomics Integrative Analysis.
Jun-Rong Zhang · Ping Hou · Xiao-Jie Wang · Zong-Qi Weng · Xin-Chang Shang-Guan · Hui Wang · Fang You · Bing-Qiang Lin · Zheng-Yuan Huang · Xian-Qiang Chen
Frontiers in immunology · 2021 doi:10.3389/fimmu.2021.742358
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Experiment
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Analysis
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Complete file
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Due to the low tumor mutation burden and low proportion of tumor-infiltrating lymphocytes in the microenvironment of most patients, innovative immunotherapeutic approaches need to be identified.\nMethods: Using the TCGA-COAD dataset (n = 514), we identified TNFRSF11B as a prognostic factor of colon cancer. An immunohistochemistry (IHC) dataset (n = 86), 290 single colorectal cancer cells (GSE81861), and 31 paired colon cancer transcriptional datasets were further applied to validate the function of TNFRSF11B, which was confirmed via fluorescence-activated cell sorting (FACS) analysis.\nResults: A risk score system consisting of eight immune-related genes (IRGs) (FGFR2, ZC3HAV1L, TNFRSF11B, CD79A, IGHV3-11, IGHV3-21, IGKV2D-30, and IGKV6D-21) was constructed to predict the prognosis of colon cancer patients. Only TNFRSF11B was closely correlated with late-stage lymph node metastasis and worse survival outcomes (p = 0.010, p = 0.014, and p = 0.0061). In our IHC dataset, 72.09% (62/86) of the colon cancer patients had TNFRSF11B overexpression with significantly shorter overall survival times (p = 0.072). High TNFRSF11B expression typically had a later TNM stage (p = 0.067), a higher frequency of lymph node (p = 0.029) and lymphovascular (p = 0.007) invasion, and a higher incidence of pneumonia (p = 0.056) than their counterparts. The expression of six genes (KRT18, ARPC5L, ACTG1, ARPC2, EZR, and YWHAZ) related to pathogenic E. coli infection was simultaneously increased with TNFRSF11B overexpression via gene set enrichment analysis (GSEA). These genes are involved in the regulation of the actin cytoskeleton, shigellosis, bacterial invasion of epithelial cells, and Salmonella infection. Finally, only activated memory CD4+ T cells (p = 0.017) were significantly decreased in the high TNFRSF11B expression group via CIBERSORT comparison, which was confirmed by TIMER2.0 analysis of the TCGA-COAD dataset. We also performed FACS analysis to show that TNFRSF11B decreased the infiltration of central memory CD4+ T cells and effector memory CD4+ T cells in the colorectal cancer microenvironment (all p <0.001).\nConclusion: TNFRSF11B acts as a prognostic factor for colon cancer patients and could affect the colon cancer immune response. TNFRSF11B was closely related to lymph node invasion and pathogenic E. coli. infection, which may negatively affect memory-activated CD4+ T cell infiltration in colon cancer.", "claims": [{"id": "claim-method", "statement": "Through Kaplan–Meier analysis, the long-term survival outcome was calculated, and the independent risk factors were identified by the Cox proportional hazards regression model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34938284", "locator": "sections[9] \"Statistics\" paragraph 2", "quote": "Through Kaplan–Meier analysis, the long-term survival outcome was calculated, and the independent risk factors were identified by the Cox proportional hazards regression model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: NCBI SRA database, SUB10070043.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34938284", "locator": "sections[18] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. 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"GSM2181349", "GSM2181350", "GSM2181351", "GSM2181352", "GSM2181353", "GSM2181354", "GSM2181355", "GSM2181356", "GSM2181357", "GSM2181358", "GSM2181359", "GSM2181360", "GSM2181361", "GSM2181362", "GSM2181363", "GSM2181364", "GSM2181365", "GSM2181366", "GSM2181367", "GSM2181368", "GSM2181369", "GSM2181370", "GSM2181371", "GSM2181372", "GSM2181373", "GSM2181374", "GSM2181375"], "sample_count": 1220, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE81861 not downloaded", "asset:data:geo:GSE81861 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": 1.0, "band": "verbatim", "quote": "Through Kaplan–Meier analysis, the long-term survival outcome was calculated, and the independent risk factors were identified by the Cox proportional hazards regression model."}}], "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": ["GSE81861"], "resolved_accessions": ["GSE81861"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: NCBI SRA database, SUB10070043."], "basis": "The paper names GSE81861 in CancerSEA 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:34938284", "data:geo:GSE81861"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE81861"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:12:31Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10316, "completion_tokens": 1930, "cached_tokens": 188}}, "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:34938284", "type": "paper", "label": "pmid:34938284"}, {"id": "source:pmid:34938284", "type": "manuscript", "label": "PMID 34938284 full text"}, {"id": "data:geo:GSE81861", "type": "dataset", "label": "GEO GSE81861"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34938284", "type": "paper", "label": "pmid:34938284"}, {"id": "source:pmid:34938284", "type": "manuscript", "label": "PMID 34938284 full text"}, {"id": "data:geo:GSE81861", "type": "dataset", "label": "GEO GSE81861"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34938284", "type": "extraction", "used": ["source:pmid:34938284"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE81861", "type": "accession_resolution", "used": ["data:geo:GSE81861"], "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:34938284", "parent_hash": "sha256:90b8e4f7a61d333f349309a424f4d03853ee96a5a4e5e06dd65e19435d914b88", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE81861 licence not read", "asset:data:geo:GSE81861 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["B as a prognostic factor of colon cancer. An immunohistochemistry (IHC) dataset (n = 86), 290 single colorecta", "or of colon cancer. An immunohistochemistry (IHC) dataset (n = 86), 290 single colorectal can", "= 0.010, p = 0.014, and p = 0.0061). In our IHC dataset, 72.09% (62/86) of the colon cancer", "s (B–D) by the Human Protein Atlas database (IHC staining) **** indicates a P value<0.0001.Cl"], "order_basis": "paper_text_order:451", "id": "assay:1"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["med via fluorescence-activated cell sorting (FACS) analysis. Results: A risk score system cons", "of the TCGA-COAD dataset. We also performed FACS analysis to show that TNFRSF11B decreased th", "nction of TNFRSF11B, which was confirmed via fluorescence-activated cell sorting (FACS) analysis. Results: A risk score syste", "ich was confirmed via fluorescence-activated cell sorting (FACS) analysis. Results: A risk score syste"], "order_basis": "paper_text_order:679", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ymphocytes were obtained. Cells with 1 µg/ml mouse anti-human CD28 PerCP-Cyanine5.5 mAb (eBiosc", "in a 96-well plate precoated with 0.2 µg/ml mouse anti-human CD3 mAb Alexa Fluor® 488 (eBiosci", "3D12), PE-Cyanine7, eBioscience #25-1979-42; mouse anti-human CD45RA BV421, eBioscience #25-197"], "order_basis": "paper_text_order:2883", "id": "assay:3"}, {"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": 1.0, "evidence": ["Through Kaplan–Meier analysis, the long-term survival outcome was calculated, and the independent risk factors were identified by the Cox proportional hazards regression model."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}