Identification of Immune Hub Genes in Obese Postmenopausal Women Using Microarray and Single-Cell RNA Seq Data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40725440", "kind": "science-record", "revision": 4, "content_hash": "sha256:271c22b1132380e38d84fb8b06faea31905e9a3b60b97dc814ef848d3de6ea7e", "created_at": "2026-11-01T20:30:49Z", "updated_at": "2026-11-01T22:56:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Immune Hub Genes in Obese Postmenopausal Women Using Microarray and Single-Cell RNA Seq Data.", "doi": "10.3390/genes16070783", "pmid": "40725440", "authors": ["Fu-Rong Zhang", "Xuan Lu", "Jia-Li Li", "Yu-Xin Li", "Wei-Wei Pang", "Ning Wang", "Kun Liu", "Qian-Qian Zhang", "Yun Deng", "Qin Zeng", "Xiao-Chao Qu", "Xiang-Ding Chen", "Hong-Wen Deng", "Li-Jun Tan"], "journal": "Genes", "year": 2025, "abstract": "Background: Obesity is characterized by a chronic state of low-grade inflammation. Investigating immune-critical genes and their biological functions in the adipose tissue of postmenopausal obese women is crucial for elucidating the underlying mechanisms of immune dysregulation associated with obesity. Methods: In this study, microarray (GSE151839) and single-cell RNA-seq (GSE176171) datasets were obtained from the Gene Expression Omnibus (GEO). For microarray data analysis, weighted gene co-expression network analysis (WGCNA), protein-protein interaction network (PPI) analysis, and immune infiltration analysis (ssGSEA) were employed to identify obesity-related immune-critical genes. Subsequently, the candidate genes were validated using scRNA-seq data to explore their expression patterns at the single-cell level. Finally, the expression levels of these immune-critical genes were experimentally verified in adipose tissue from obese and control zebrafish models using RT-qPCR. Results: Analysis of microarray data through WGCNA, PPI and ssGSEA identified 16 obesity-related immune-critical genes, including IL7R, CD3E, CD2, CCR5, CD3D, MS4A1, TRAT1, SLAMF8, CCL3L1, SPP1, CCL5, IL2RG, CD3G, TLR8, ITK, and CCL3. Differential expression of SPP1, ITK and CCL5 was confirmed in scRNA-seq data, with ITK and CCL5 showing distinct expression patterns in natural killer (NK) cells. Furthermore, RT-qPCR analysis revealed upregulation of SPP1 and ITK in adipose tissue of obese zebrafish compared to lean controls. Conclusions: This study identifies SPP1, ITK and CCL5 as key immune hub genes in the adipose tissue of postmenopausal obese women, with NK cells playing a significant role in adipose tissue inflammation through the expression of these genes. These findings provide novel insights into potential therapeutic targets for the prevention and treatment of obesity in postmenopausal women.", "claims": [{"id": "claim-method", "statement": "Limma package [19] was used to screen DEGs in dataset GSE151839 with the absolute difference multiple greater than 1 (|logFC(Foldchange)| > 1) and p value < 0.05 after correction.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40725440", "locator": "sections[6] \"2.4. 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Methods: In this study, microarray (GSE151839) and single-cell RNA-seq (GSE1761", "from the Gene Expression Omnibus (GEO). For microarray data analysis, weighted gene co-expression n", "h models using RT-qPCR. Results: Analysis of microarray data through WGCNA, PPI and ssGSEA identifie"], "order_basis": "paper_text_order:26", "id": "assay:1"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["s: In this study, microarray (GSE151839) and single-cell RNA-seq (GSE176171) datasets were obtained from the", "ly, the candidate genes were validated using scRNA-seq data to explore their expression patterns at", "ssion of SPP1, ITK and CCL5 was confirmed in scRNA-seq data, with ITK and CCL5 showing distinct exp", "eria. Further validation was performed using single-cell RNA-seq (scRNA-seq) data to identify immune cells in"], "order_basis": "paper_text_order:422", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["rom obese and control zebrafish models using RT-qPCR. Results: Analysis of microarray data throug", "s in natural killer (NK) cells. Furthermore, RT-qPCR analysis revealed upregulation of SPP1 and I", "obese and control zebrafish models using RT-qPCR. Results: Analysis of microarray data throug", "n natural killer (NK) cells. 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