Identification of a novel immune infiltration-related gene signature, MCEMP1, for coronary artery disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39346078", "kind": "science-record", "revision": 4, "content_hash": "sha256:ea080f0df01fd8c59760b64870c2fe9fbb1c86e7666b86b828b41b0eae8ac2dd", "created_at": "2026-11-01T20:29:33Z", "updated_at": "2026-11-01T22:55:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a novel immune infiltration-related gene signature, MCEMP1, for coronary artery disease.", "doi": "10.7717/peerj.18135", "pmid": "39346078", "authors": ["Wei Ye", "Bo Shen", "Qizhu Tang", "Chengzhi Fang", "Lei Wang", "Lili Xie", "Qi He"], "journal": "PeerJ", "year": 2024, "abstract": "Background: This study aims to identify a novel gene signature for coronary artery disease (CAD), explore the role of immune cell infiltration in CAD pathogenesis, and assess the cell function of mast cell-expressed membrane protein 1 (MCEMP1) in human umbilical vein endothelial cells (HUVECs) treated with oxidized low-density lipoprotein (ox-LDL).\nMethods: To identify differentially expressed genes (DEGs) of CAD, datasets GSE24519 and GSE61145 were downloaded from the Gene Expression Omnibus (GEO) database using the R \"limma\" package with p < 0.05 and |log2 FC| > 1. Gene ontology (GO) and pathway analyses were conducted to determine the biological functions of DEGs. Hub genes were identified using support vector machine-recursive feature elimination (SVM-RFE) and least absolute shrinkage and selection operator (LASSO). The expression levels of these hub genes in CAD were validated using the GSE113079 dataset. CIBERSORT program was used to quantify the proportion of immune cell infiltration. Western blot assay and qRT-PCR were used to detect the expression of hub genes in ox-LDL-treated HUVECs to validate the bioinformatics results. Knockdown interference sequences for MCEMP1 were synthesized, and cell proliferation and apoptosis were examined using a CCK8 kit and Muse® Cell Analyzer, respectively. The concentrations of IL-1β, IL-6, and TNF-α were measured with respective enzyme-linked immunosorbent assay (ELISA) kits.\nResults: A total of 73 DEGs (four down-regulated genes and 69 up-regulated genes) were identified in the metadata (GSE24519 and GSE61145) cohort. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis results indicated that these DEGs might be associated with the regulation of platelet aggregation, defense response or response to bacterium, NF-kappa B signaling pathway, and lipid and atherosclerosis. Using SVM-RFE and LASSO, seven hub genes were obtained from the metadata. The upregulated expression of DIRC2 and MCEMP1 in CAD was confirmed in the GSE113079 dataset and in ox-LDL-treated HUVECs. The associations between the two hub genes (DIRC2 and MCEMP1) and the 22 types of immune cell infiltrates in CAD were found. MCEMP1 knockdown accelerated cell proliferation and suppressed cell apoptosis for ox-LDL-treated HUVECs. Additionally, MCEMP1 knockdown appeared to decrease the expression of inflammatory factors IL-1β, IL-6, and TNF-α.\nConclusions: The results of this study indicate that MCEMP1 may play an important role in CAD pathophysiology.", "claims": [{"id": "claim-method", "statement": "DEGs between CAD samples and normal samples were identified using the R “limma” package (https://bioconductor.org/packages/release/bioc/html/limma.html) with a significance threshold of p < 0.05 and |log2 FC| > 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39346078", "locator": "sections[3] \"Screening and enrichment analysis of differentially expressed genes (DEGs)\" paragraph 3", "quote": "DEGs between CAD samples and normal samples were identified using the R “limma” package (https://bioconductor.org/packages/release/bioc/html/limma.html) with a significance threshold of p < 0.05 and |log2 FC| > 1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files.\nThe flow cytometry data is available at Zenodo: Bo, S. (2024). Identification of A Novel Immune Infiltration-related Gene Signature MCEMP1 for coronary artery disease. Zenodo. https://doi.org/10.5281/zenodo.11171072.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39346078", "locator": "sections[32] \"Data Availability Statement\" paragraphs 1-4", "quote": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files.\nThe flow cytometry data is available at Zenodo: Bo, S. (2024). Identification of A Novel Immune Infiltration-related Gene Signature MCEMP1 for coronary artery disease. Zenodo. https://doi.org/10.5281/zenodo.11171072."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The results, shown in Figs. 6C–6E, indicated that MCEMP1 knockdown promoted cell proliferation (p < 0.01, Fig. 6C) but inhibited apoptosis (p < 0.001, Fig. 6D).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39346078", "locator": "sections[17] \"Low expression of MCEMP1 promoted the dysfunction of ox-LDL-treated HUVECs\" paragraph 4", "quote": "The results, shown in Figs. 6C–6E, indicated that MCEMP1 knockdown promoted cell proliferation (p < 0.01, Fig. 6C) but inhibited apoptosis (p < 0.001, Fig. 6D)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The results, shown in Figs. 6C–6E, indicated that MCEMP1 knockdown promoted cell proliferation (p < 0.01, Fig. 6C) but inhibited apoptosis (p < 0.001, Fig. 6D).", "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:39346078"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39346078", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.18135", "sha256": "sha256:9237784f79f92f8468435cdc6187b16a216a45da5db502d412efd4e2615354e4", "bytes": 55293, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.18135", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11438437", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "DEGs between CAD samples and normal samples were identified using the R “limma” package (https://bioconductor.org/packages/release/bioc/html/limma.html) with a significance threshold of p < 0.05 and |log2 FC| > 1."}}, {"id": "method-2", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "support vector machine"}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files.\nThe flow cytometry data is available at Zenodo: Bo, S. (2024). Identification of A Novel Immune Infiltration-related Gene Signature MCEMP1 for coronary artery disease. Zenodo. https://doi.org/10.5281/zenodo.11171072."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:39346078"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:33:41Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16532, "completion_tokens": 3941, "cached_tokens": 264}}, "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:39346078", "type": "paper", "label": "pmid:39346078"}, {"id": "source:pmid:39346078", "type": "manuscript", "label": "PMID 39346078 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39346078", "type": "paper", "label": "pmid:39346078"}, {"id": "source:pmid:39346078", "type": "manuscript", "label": "PMID 39346078 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39346078", "type": "extraction", "used": ["source:pmid:39346078"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:39346078", "parent_hash": "sha256:33fd51d5aa03a21732268bf1667cdcd1d2500bf72bb7fbdee3591a59fd5c95ef", "fork_of": null, "generation": 3}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"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": ["the proportion of immune cell infiltration. Western blot assay and qRT-PCR were used to detect the ex", "P1 in HUVECs was detected by qRT-PCR (A) and Western blot (B). *p < 0.05; **p < 0.01; ***p < 0.001. HU", "5/supp-5 Supplemental Information 6Raw data: Western blot experiments.10.7717/peerj.18135/supp-6"], "order_basis": "paper_text_order:1070", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["VECs to validate the bioinformatics results. Knockdown interference sequences for MCEMP1 were synth", "e cell infiltrates in CAD were found. MCEMP1 knockdown accelerated cell proliferation and suppresse", "ox-LDL-treated HUVECs. Additionally, MCEMP1 knockdown appeared to decrease the expression of infla", "j.18135/supp-2 Supplemental Information 3The knockdown efficiency of MCEMP1.The expression of MCEMP"], "order_basis": "paper_text_order:1213", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["were synthesized, and cell proliferation and apoptosis were examined using a CCK8 kit and Muse® Cel", "rated cell proliferation and suppressed cell apoptosis for ox-LDL-treated HUVECs. Additionally, MCE", "feration and apoptosis were examined using a CCK8 kit and Muse® Cell Analyzer, respectively. T"], "order_basis": "paper_text_order:1302", "id": "assay:3"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["espective enzyme-linked immunosorbent assay (ELISA) kits. Results: A total of 73 DEGs (four dow", "L-6, and TNF-α were measured with respective enzyme-linked immunosorbent assay (ELISA) kits. Results: A total of 73 DEGs (f"], "order_basis": "paper_text_order:1457", "id": "assay:4"}, {"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": ["DEGs between CAD samples and normal samples were identified using the R “limma” package (https://bioconductor.org/packages/release/bioc/html/limma.html) with a significance threshold of p < 0.05 and |log2 FC| > 1."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}