Differential Gene Expression and Immune Cell Infiltration in Carotid Intraplaque Hemorrhage Identified Using Integrated Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35656397", "kind": "science-record", "revision": 5, "content_hash": "sha256:aae226b0abd669d2c0b2706f3a583bf03d7ece410706645090a076758c4ec8ab", "created_at": "2026-11-01T18:14:36Z", "updated_at": "2026-11-01T22:49:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Differential Gene Expression and Immune Cell Infiltration in Carotid Intraplaque Hemorrhage Identified Using Integrated Bioinformatics Analysis.", "doi": "10.3389/fcvm.2022.818585", "pmid": "35656397", "authors": ["Xiaoshuo Lv", "Feng Wang", "Mingsheng Sun", "Congrui Sun", "Xueqiang Fan", "Bo Ma", "Yuguang Yang", "Zhidong Ye", "Peng Liu", "Jianyan Wen"], "journal": "Frontiers in cardiovascular medicine", "year": 2022, "abstract": "Background: Intraplaque hemorrhage (IPH) is an important feature of unstable plaques and an independent risk factor for cardiovascular events. However, the molecular mechanisms contributing to IPH are incompletely characterized. We aimed to identify novel biomarkers and interventional targets for IPH and to characterize the role of immune cells in IPH pathogenesis.\nMethods: The microarray dataset GSE163154 which contain IPH and non-IPH plaque samples was obtained from the Gene Expression Omnibus (GEO). R software was adopted for identifying differentially expressed genes (DEGs) and conducting functional investigation. The hub genes were carried by protein-protein interaction (PPI) network and were validated by the GSE120521 dataset. CIBERSORT deconvolution was used to determine differential immune cell infiltration and the relationship of immune cells and hub genes. We confirmed expression of proteins encoded by the hub genes by immunohistochemistry and western blotting in 8 human carotid endarterectomy samples with IPH and 8 samples without IPH (non-IPH).\nResults: We detected a total of 438 differentially expressed genes (DEGs), of which 248 were upregulated and 190 were downregulated. DEGs were mainly involved in inflammatory related pathways, including neutrophil activation, neutrophil degranulation, neutrophil-mediated immunity, leukocyte chemotaxis, and lysosomes. The hub genes found through the method of degree in the PPI network showed that ITGB2 and ITGAM might play an important role in IPH. Receiver operating characteristic (ROC) results also showed a good performance of these two genes in the test and validation dataset. We found that the proportions of infiltrating immune cells in IPH and non-IPH samples differed, especially in terms of M0 and M2 macrophages. Immunohistochemistry and western blotting analysis showed that expression levels of ITGB2 and ITGAM increased significantly in carotid atherosclerotic plaques with IPH.\nConclusion: ITGB2 and ITGAM are key hub genes of IPH and may play an important role in the biological process of IPH. Our findings advance our understanding of the underlying mechanisms of IPH pathogenesis and provide valuable information and directions for future research into novel targets for IPH diagnosis and immunotherapy.", "claims": [{"id": "claim-method", "statement": "The limma package in R was used to normalize and screen DEGs between non-IPH samples and IPH samples. DEGs with an adjusted false discovery rate (FDR) p < 0.05 and |log2 fold change (FC)| >1 were considered significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35656397", "locator": "sections[5] \"Identification of DEGs\" paragraph 2", "quote": "The limma package in R was used to normalize and screen DEGs between non-IPH samples and IPH samples. DEGs with an adjusted false discovery rate (FDR) p < 0.05 and |log2 fold change (FC)| >1 were considered significant."}], "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:35656397", "locator": "sections[24] \"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": "A total of 438 DEGs were screened, with an adjusted p-value of <0.05 and | log2 (fold-change) | >1 as thresholds.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35656397", "locator": "sections[15] \"Identification of DEGs\" paragraph 2", "quote": "A total of 438 DEGs were screened, with an adjusted p-value of <0.05 and | log2 (fold-change) | >1 as thresholds."}, {"asset": "source:pmid:35656397", "locator": "sections[15] \"Identification of DEGs\" paragraph 2", "quote": "A total of 248 upregulated and 190 downregulated DEGs were identified in IPH samples when compared to non-IPH samples, as shown by volcano plot (Figure 3A) and heatmap (Figure 3B), while a detailed summary was listed in Supplementary Table S1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 438 DEGs were screened, with an adjusted p-value of <0.05 and | log2 (fold-change) | >1 as thresholds.", "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:35656397"], "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:GSE120521"], "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:GSE120521"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35656397", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcvm.2022.818585", "sha256": "sha256:9bcd880170f90980f3c71d31237a0113ce5d5d7ff01416fa7a613cfa700a31a6", "bytes": 36581, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcvm.2022.818585", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9152291", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE120521", "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=GSE120521", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE120521", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:35656397", "data:geo:GSE120521"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE120521"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:48:50Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10104, "completion_tokens": 1343, "cached_tokens": 265}}, "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:35656397", "type": "paper", "label": "pmid:35656397"}, {"id": "source:pmid:35656397", "type": "manuscript", "label": "PMID 35656397 full text"}, {"id": "data:geo:GSE120521", "type": "dataset", "label": "GEO GSE120521"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35656397", "type": "paper", "label": "pmid:35656397"}, {"id": "source:pmid:35656397", "type": "manuscript", "label": "PMID 35656397 full text"}, {"id": "data:geo:GSE120521", "type": "dataset", "label": "GEO GSE120521"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35656397", "type": "extraction", "used": ["source:pmid:35656397"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE120521", "type": "accession_resolution", "used": ["data:geo:GSE120521"], "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:35656397", "parent_hash": "sha256:559bc166bac2ce95bfd7867ec481579d75ab8065d33316d210df2b887b515499", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE120521 licence not read", "asset:data:geo:GSE120521 not downloaded", "asset:data:geo:GSE163154 licence not read", "asset:data:geo:GSE163154 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["mune cells in IPH pathogenesis. Methods: The microarray dataset GSE163154 which contain IPH and non-"], "order_basis": "paper_text_order:481", "id": "assay:1"}, {"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": ["sion of proteins encoded by the hub genes by immunohistochemistry and western blotting in 8 human carotid enda", "specially in terms of M0 and M2 macrophages. Immunohistochemistry and western blotting analysis showed that ex", ". (C) Typical micrographs of ITGAM and ITGB2 immunohistochemical staining, macroscopic, and microscopic views", "Histograms show the quantitative results of immunohistochemical staining. ITGAM and ITGB2 expression were si"], "order_basis": "paper_text_order:1043", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["by the hub genes by immunohistochemistry and western blotting in 8 human carotid endarterectomy samples wi", "and M2 macrophages. Immunohistochemistry and western blotting analysis showed that expression levels of IT", "ignificantly increased in the IPH group. (E) Western blotting was used to determine the protein expression", "er than that of non-IPH samples (Figure 8D). Western blotting was used to evaluate the protein expression"], "order_basis": "paper_text_order:1068", "id": "assay:3"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The limma package in R was used to normalize and screen DEGs between non-IPH samples and IPH samples. DEGs with an adjusted false discovery rate (FDR) p < 0.05 and |log2 fold change (FC)| >1 were considered significant."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}