Construction of LncRNA-mediated CeRNA network for investigating the immune pathogenesis of myocardial infarction.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38457553", "kind": "science-record", "revision": 5, "content_hash": "sha256:fc28db77d1f332a473803ec89ac4be9a916e1aae8154655b64b24ca1be1d3bdf", "created_at": "2026-11-01T19:20:23Z", "updated_at": "2026-11-01T22:53:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction of LncRNA-mediated CeRNA network for investigating the immune pathogenesis of myocardial infarction.", "doi": "10.1097/MD.0000000000037413", "pmid": "38457553", "authors": ["Dongmei Wei", "Yuanting Meng", "Hua Fan", "Yang Sun", "Rongtao Chen"], "journal": "Medicine", "year": 2024, "abstract": "BACKGROUND: Myocardial infarction (MI) is a cardiovascular disease that seriously threatens human health. However, an immune-related competitive endogenous RNA (ceRNA) network has not been reported in MI.\nMETHODS: The GSE66360, GSE19339, GSE97320, GSE61741, and GSE168281 datasets were acquired from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) from MI patients and healthy controls were screened and an immune-related ceRNA network was constructed. Furthermore, the key long noncoding RNAs(lncRNAs) highly related to the immune mechanism of MI were identified utilizing the random walk with restart algorithm. Finally, the expression of the hub genes was further verified in the GSE66360, GSE19339, and GSE97320 datasets, and quantitativereal-time polymerase chain reaction (qRT-PCR) was performed for the MI patients and healthy controls.\nRESULTS: A total of 184 differentially expressed immune-related genes(DE-IRGs) and 432 DE-miRNAs were obtained, and an immune-related ceRNA network comprising 1421 lncRNAs, 61 DE-miRNAs, and 139 DE-IRGs was constructed. According to the order of stress, betweenness, and closeness, NEAT1, KCNQ1OT1, and XIST were identified as key lncRNAs. Moreover, random walk with restart analysis also suggested that NEAT1, KCNQ1OT1, and XIST are key lncRNAs. Subsequently, a ceRNA network of 10 hub genes and 3 lncRNAs was constructed. Finally, we found that the expression of FCER1G and TYROBP significantly differed between MI patients and control individuals in the GSE66360, GSE19339, and GSE97320 datasets. qRT-PCR revealed that the expression of NEAT1, KCNQ1OT1, XIST, FCER1G, and TYROBP was significantly elevated in MI tissue samples compared to healthy control tissue samples.\nCONCLUSION: NEAT1, KCNQ1OT1, XIST, FCER1G, and TYROBP are involved in MI and can be used as molecular biomarkers for the screening and diagnosis of MI. Furthermore, the immune system plays an essential role in the onset and progression of MI.", "claims": [{"id": "claim-method", "statement": "The limma package (version 3.46.0)[16] was applied to select the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) between the MI and control samples in the GSE66360 and GSE61741 datasets with the following filters: (P < .05, and |log2fold change| ≥ 1.0) (MI vs control).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38457553", "locator": "sections[4] \"2.2. Differential expression analysis\" paragraph 2", "quote": "The limma package (version 3.46.0)[16] was applied to select the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) between the MI and control samples in the GSE66360 and GSE61741 datasets with the following filters: (P < .05, and |log2fold change| ≥ 1.0) (MI vs control)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38457553", "locator": "sections[24] \"fn-group\" paragraph 1", "quote": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "NEAT1, KCNQ1OT1, XIST, FCER1G, and TYROBP are involved in MI and can be used as molecular biomarkers for the screening and diagnosis of MI.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38457553", "locator": "sections[0] \"Abstract\" paragraph 6", "quote": "NEAT1, KCNQ1OT1, XIST, FCER1G, and TYROBP are involved in MI and can be used as molecular biomarkers for the screening and diagnosis of MI."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "NEAT1, KCNQ1OT1, XIST, FCER1G, and TYROBP are involved in MI and can be used as molecular biomarkers for the screening and diagnosis of MI.", "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:38457553"], "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:GSE168281"], "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:GSE168281"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38457553", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000037413", "sha256": 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author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5135512", "GSM5135513", "GSM5135514", "GSM5135515", "GSM5135516", "GSM5135517", "GSM5135518", "GSM5135519", "GSM5135520"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Uncovering potential lncRNAs and mRNAs in progression from acute myocardial infarction to myocardial fibrosis to heart failure", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE19339", "role": "raw", "format": "geo-series", "media_type": 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in thrombus-derived white blood cells of patients with acute coronary syndrome", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE61741", "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=GSE61741", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE61741", "version": null, "note": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.", 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