Comprehensive Landscape of Immune Infiltration and Aberrant Pathway Activation in Ischemic Stroke.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35140708", "kind": "science-record", "revision": 4, "content_hash": "sha256:8694a2ee5647580d4ad05ddf2e4cfe1032956d35b1c35f7e912ee40160d5d741", "created_at": "2026-11-01T17:36:53Z", "updated_at": "2026-11-01T22:05:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive Landscape of Immune Infiltration and Aberrant Pathway Activation in Ischemic Stroke.", "doi": "10.3389/fimmu.2021.766724", "pmid": "35140708", "authors": ["Rongrong Liu", "Pingping Song", "Xunhu Gu", "Weidong Liang", "Wei Sun", "Qian Hua", "Yusheng Zhang", "Zhengang Qiu"], "journal": "Frontiers in immunology", "year": 2021, "abstract": "Ischemic stroke (IS) is a multifactorial disease caused by the interaction of multiple environmental and genetic risk factors, and it is the most common cause of disability. The immune microenvironment and inflammatory response participate in the whole process of IS occurrence and development. Therefore, the rational use of relevant markers or characteristic pathways in the immune microenvironment will become one of the important therapeutic strategies for the treatment of IS. We collected peripheral blood samples from 10 patients diagnosed with IS at the First Affiliated Hospital of Gannan Medical University and First Affiliated Hospital, Jinan\" University, and from 10 normal people. The GSE16561 dataset was downloaded from the Gene Expression Omnibus (GEO) database. xCell, gene set enrichment analysis (GSEA), single-sample GSEA (ssGSEA) and immune-related gene analysis were used to evaluate the differences in the immune microenvironment and characteristic pathways between the IS and control groups of the two datasets. xCell analysis showed that the IS-24h group had significantly reduced central memory CD8+ T cell, effector memory CD8+ T cell, B cell and Th1 cell scores and significantly increased M1 macrophage and macrophage scores. GSEA showed that the IS-24h group had significantly increased inflammation-related pathway activity(myeloid leukocyte activation, positive regulation of tumor necrosis factor biosynthetic process, myeloid leukocyte migration and leukocyte chemotaxis), platelet-related pathway activity(platelet activation, signaling and aggregation; protein polymerization; platelet degranulation; cell-cell contact zone) and pathology-related pathway activity (ERBB signaling pathway, positive regulation of ERK1 and ERK2 cascade, vascular endothelial growth factor receptor signaling pathway, and regulation of MAP kinase activity). Immune-related signature analysis showed that the macrophage signature, antigen presentation-related signature, cytotoxicity-related signature, B cell-related signature and inflammation-related signature were significantly lower in the IS-24h group than in the control group. In this study, we found that there were significant differences in the immune microenvironment between the peripheral blood of IS patients and control patients, as shown by the IS group having significantly reduced CD8+ Tcm, CD8+ Tem, B cell and Th1 cell scores and significantly increased macrophage and M1 macrophage scores. Additionally, inflammation-related, pathological, and platelet-related pathway activities were significantly higher in the IS group than in the control group.", "claims": [{"id": "claim-method", "statement": "For GSE16561, the Mann-Whitney U test was used to evaluate differences in continuous variables between the two groups. For the Local-IS dataset, the Mann-Whitney U test was used to evaluate differences in continuous variables between the IS-24h and control groups or the IS-36h and control groups; the paired Mann-Whitney U test was used to compare continuous variables between the IS-36h and IS-24h groups (paired samples).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35140708", "locator": "sections[7] \"Statistical Analysis\" paragraph 2", "quote": "For GSE16561, the Mann-Whitney U test was used to evaluate differences in continuous variables between the two groups. For the Local-IS dataset, the Mann-Whitney U test was used to evaluate differences in continuous variables between the IS-24h and control groups or the IS-36h and control groups; the paired Mann-Whitney U test was used to compare continuous variables between the IS-36h and IS-24h groups (paired samples)."}], "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 in the article/ Supplementary Material .", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35140708", "locator": "sections[14] \"Data Availability Statement\" paragraph 2", "quote": "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 in the article/ Supplementary Material ."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In this study, we found that there were significant differences in the immune microenvironment between the peripheral blood of IS patients and control patients, as shown by the IS group having significantly reduced CD8+ Tcm, CD8+ Tem, B cell and Th1 cell scores and significantly increased macrophage and M1 macrophage scores.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35140708", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In this study, we found that there were significant differences in the immune microenvironment between the peripheral blood of IS patients and control patients, as shown by the IS group having significantly reduced CD8+ Tcm, CD8+ Tem, B cell and Th1 cell scores and significantly increased macrophage and M1 macrophage scores."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "In this study, we found that there were significant differences in the immune microenvironment between the peripheral blood of IS patients and control patients, as shown by the IS group having significantly reduced CD8+ Tcm, CD8+ Tem, B cell and Th1 cell scores and significantly increased macrophage and M1 macrophage scores.", "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:35140708"], "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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We collected peripheral blood samples from 10 patients diagnosed with IS at the First A"], "order_basis": "paper_text_order:560", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["al. (19). For a detailed description of the RNA-seq analysis of the samples, please refer to the"], "order_basis": "paper_text_order:3649", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["data file. Supplementary Table 3Primers for qPCR.Click here for additional data file. 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