Immune cell infiltration and the genes associated with ligamentum flavum hypertrophy: Identification and validation.

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The aim of the current study was to identify the differentially expressed genes (DEGs) in LFH and the molecular mechanisms underlying the development of and immune responses to LFH. The gene expression omnibus (GEO) database was used to obtain the GSE113212 dataset, and the DEGs were derived from microarray data. To identify critical genes and signaling pathways, gene ontology enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network analyses were performed, followed by immune cell infiltration and Friends analyses using the retrieved datasets. The results were validated using quantitative real-time PCR. The 1530 DEGs identified comprised 971 upregulated and 559 downregulated genes. KEGG analysis revealed that DEGs were mostly enriched in the PI3K-Akt signaling pathway, while PPI network analysis identified tumor necrosis factor, interleukin (IL)-6, IL-10, epidermal growth factor receptor, and leptin as important nodes, which was validated by qPCR and IHC in human LFH tissues in vitro. A significant positive correlation was found between key LFH immune-related DEGs and several immune cell types, including T and B cells. The findings of the present study might lead to novel therapeutic targets and clinical approaches, as they provide insights into the molecular mechanisms of LFH.", "claims": [{"id": "claim-method", "statement": "The limma package (Ritchie et al., 2015) was also used to examine group variances based on data grouping information.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36036007", "locator": "sections[3] \"Data collection and assessment of differentially expressed genes\" paragraph 3", "quote": "The limma package (Ritchie et al., 2015) was also used to examine group variances based on data grouping information."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed in this study can be found in the GSE113212 data set of the Gene Expression Omnibus database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36036007", "locator": "sections[26] \"Data availability statement\" paragraph 2", "quote": "The datasets analyzed in this study can be found in the GSE113212 data set of the Gene Expression Omnibus database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The 1530 DEGs identified comprised 971 upregulated and 559 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36036007", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The 1530 DEGs identified comprised 971 upregulated and 559 downregulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The 1530 DEGs identified comprised 971 upregulated and 559 downregulated genes.", "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:36036007"], "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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