A novel lncRNA-miRNA-mRNA triple network identifies lncRNA XIST as a biomarker for acute myocardial infarction.

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The GSE34198 dataset from the Gene Expression Omnibus (GEO) database, which comprised 49 specimens from individuals with AMI and 47 specimens from controls, was extracted and analysed using the weighted gene co-expression network analysis (WGCNA) package. Twenty-seven key genes were identified through a combination of the degree and gene significance (GS) values, and the CDC42 (degree = 64), JAK2 (degree = 41), and CHUK (degree = 30) genes were identified as having the top three-degree values among the 27 genes. Potential interactions between lncRNA, miRNAs and mRNAs were predicted using the starBase V3.0 database, and a lncRNA-miRNA-mRNA triple network containing the lncRNA XIST, twenty-one miRNAs and three hub genes (CDC42, JAK2 and CHUK) was identified. RT-qPCR validation showed that the expression of the JAK2 and CDC42 genes and the lncRNA XIST was noticeably increased in samples from patients with AMI compared to normal samples. Pearson's correlation analysis also proved that JAK2 and CDC42 expression levels correlated positively with lncRNA XIST expression levels. The area under ROC curve (AUC) of lncRNA XIST was 0.886, and the diagnostic efficacy of the lncRNA XIST was significantly better than that of JAK2 and CDC42. The results suggested that the lncRNA XIST appears to be a risk factor for AMI likely through its ability to regulate JAK2 and CDC42 gene expressions, and it is expected to be a novel and reliable biomarker for the diagnosis of AMI.", "claims": [{"id": "claim-method", "statement": "The GSE34198 dataset from the Gene Expression Omnibus (GEO) database, which comprised 49 specimens from individuals with AMI and 47 specimens from controls, was extracted and analysed using the weighted gene co-expression network analysis (WGCNA) package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35537778", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The GSE34198 dataset from the Gene Expression Omnibus (GEO) database, which comprised 49 specimens from individuals with AMI and 47 specimens from controls, was extracted and analysed using the weighted gene co-expression network analysis (WGCNA) package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene expression data were extracted from the CAD dataset GSE34198 (including 49 AMI and 48 normal samples) in the public database Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo, which is hosted on the GPL6102 Illumina human-6 v2.0 expression BeadChip platform).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35537778", "locator": "sections[15] \"CAD microarray datasets\" paragraph 2", "quote": "Gene expression data were extracted from the CAD dataset GSE34198 (including 49 AMI and 48 normal samples) in the public database Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo, which is hosted on the GPL6102 Illumina human-6 v2.0 expression BeadChip platform)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The lncRNA XIST appears to be a risk factor for AMI likely through its ability to regulate JAK2 and CDC42 gene expressions, and it is expected to be a novel and reliable biomarker for the diagnosis of AMI.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35537778", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The results suggested that the lncRNA XIST appears to be a risk factor for AMI likely through its ability to regulate JAK2 and CDC42 gene expressions, and it is expected to be a novel and reliable biomarker for the diagnosis of AMI."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The lncRNA XIST appears to be a risk factor for AMI likely through its ability to regulate JAK2 and CDC42 gene expressions, and it is expected to be a novel and reliable biomarker for the diagnosis of AMI.", "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:35537778"], "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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