Transcriptome Profiling of the Anterior Cingulate Cortex in a CFA-Induced Inflammatory Pain Model Identifies ECM-Related Genes in a Model of Rheumatoid Arthritis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41595435", "kind": "science-record", "revision": 3, "content_hash": "sha256:0efec979e49d4f224965f850becc85c9c92903703a62cae88acf580b1d454961", "created_at": "2026-11-01T20:31:33Z", "updated_at": "2026-11-01T22:15:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome Profiling of the Anterior Cingulate Cortex in a CFA-Induced Inflammatory Pain Model Identifies ECM-Related Genes in a Model of Rheumatoid Arthritis.", "doi": "10.3390/genes17010015", "pmid": "41595435", "authors": ["Guang-Xin Xie", "Jian-Mei Li", "Bai-Tong Liu", "Jiang-Tao Wang", "Lu-Shuang Xie", "Xiao-Yi Xiong", "Qiao-Feng Wu", "Shu-Guang Yu"], "journal": "Genes", "year": 2025, "abstract": "BACKGROUND: Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by persistent joint inflammation and progressive bone destruction. However, its complex pathogenesis remains poorly understood, and effective therapeutic targets are still lacking.\nOBJECTIVE: This study aimed to identify key genes associated with RA and elucidate their biological significance by integrating bioinformatic analysis with experimental validation.\nMETHODS: Whole-transcriptome data from the anterior cingulate cortex (ACC) of Complete Freund's Adjuvant (CFA)-induced inflammatory pain and control mice (GSE147216 dataset, GEO database) were collected from NCBI (National Center for Biotechnology Information). Differentially expressed genes (DEGs) were first identified. Subsequent analyses included Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, construction of a protein-protein interaction (PPI) network, and identification of hub genes using a Random Forest machine learning algorithm. Quantitative PCR (qPCR) was performed to validate gene expression levels.\nRESULTS: A total of 76 DEGs were identified, including 64 upregulated and 12 downregulated genes. Among them, Fn1 (fibronectin 1), Bgn (biglycan), and Lum (lumican) were identified as hub genes. Functional enrichment analysis revealed inflammatory responses, extracellular matrix (ECM) remodeling, and the TGF-β signaling pathway. qPCR validation confirmed significant upregulation of Fn1, Bgn, and Lum mRNA in the CFA group.\nCONCLUSIONS: This study highlights the potential roles of Fn1, Bgn, and Lum in the central sensitization associated with inflammatory pain, offering insights relevant to RA.", "claims": [{"id": "claim-method", "statement": "A Random Forest analysis was performed to rank the importance of the DEGs identified in Section 3.1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41595435", "locator": "sections[8] \"2.6. Random Forest Analysis for Gene Ranking\" paragraph 2", "quote": "A Random Forest analysis was performed to rank the importance of the DEGs identified in Section 3.1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the current study are available in the GEO database under accession number GSE147216 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147216 (accessed on 15 October 2025)).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41595435", "locator": "sections[35] \"Data Availability Statement\" paragraph 2", "quote": "The datasets analyzed during the current study are available in the GEO database under accession number GSE147216 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147216 (accessed on 15 October 2025))."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 76 DEGs were identified, including 64 upregulated and 12 downregulated genes. Among them, Fn1 (fibronectin 1), Bgn (biglycan), and Lum (lumican) were identified as hub genes. qPCR validation confirmed significant upregulation of Fn1, Bgn, and Lum mRNA in the CFA group.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41595435", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 76 DEGs were identified, including 64 upregulated and 12 downregulated genes."}, {"asset": "source:pmid:41595435", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Among them, Fn1 (fibronectin 1), Bgn (biglycan), and Lum (lumican) were identified as hub genes."}, {"asset": "source:pmid:41595435", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "qPCR validation confirmed significant upregulation of Fn1, Bgn, and Lum mRNA in the CFA group."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A total of 76 DEGs were identified, including 64 upregulated and 12 downregulated genes. Among them, Fn1 (fibronectin 1), Bgn (biglycan), and Lum (lumican) were identified as hub genes. qPCR validation confirmed significant upregulation of Fn1, Bgn, and Lum mRNA in the CFA group.", "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:41595435"], "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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