Single-Cell Transcriptome Analysis Reveals the Importance of IRF1/FSTL1 in Synovial Fibroblast Subsets for the Development of Rheumatoid Arthritis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35572839", "kind": "science-record", "revision": 5, "content_hash": "sha256:30b11271fca7471c02a8a8e4a21a81c9d5fe1d0c1bf2f1b6e3431c139c738b5c", "created_at": "2026-11-01T18:14:28Z", "updated_at": "2026-11-01T22:49:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Single-Cell Transcriptome Analysis Reveals the Importance of IRF1/FSTL1 in Synovial Fibroblast Subsets for the Development of Rheumatoid Arthritis.", "doi": "10.1155/2022/1169614", "pmid": "35572839", "authors": ["Qiang Wang", "Xia Yu", "Mingzhi Gong"], "journal": "Computational and mathematical methods in medicine", "year": 2022, "abstract": "Objectives: This study aimed to investigate the potential role of synovial fibroblasts (SFs) in the development of rheumatoid arthritis (RA) to identify potential molecular targets and provide a theoretical basis for the treatment of RA.\nMethods: GSE109449, a fibroblast transcriptome dataset of synovial tissue from RA and osteoarthritis (OA), were obtained from the GEO database. After standard cell quality control, this single-cell transcriptome data was used to perform routine single-cell analysis processes. After completing dimensionality reduction, clustering, and cell subset identification of fibroblasts, the SCENIC analysis helped calculate the significant gene regulatory networks in fibroblasts and their subsets. From these computed gene regulatory networks, the regulon in which follistatin-like protein 1 (FSTL1) resides was extracted and used to analyze the transcriptional regulatory status of fibroblasts. Finally, the gene set enrichment analysis (GSEA) was used to calculate the respective enriched gene sets of IRF1 and FSTL1.\nResults: Three SF subgroups were identified from the single-cell transcriptome analysis; SF subset 3 was more abundant in RA than in OA (p < 0.001). From the SCENIC analysis, we obtained 269 regulons and the corresponding gene regulatory networks in SF from the RA datasets. Next, we screened and obtained a regulon-containing FSTL1, where IRF1 was the major transcription factor. The top five regulons in SF subset 3 were TWIST1, MECOM, KLF6, MAFB, and RUNX1. Among the 3 SF subsets, IRF1 regulon was ranked the highest in SF subset 3. Differential analysis of pseudobulk RNA-seq showed that IRF1 was up-regulated in RA compared to OA. Between the three SF subgroups, IRF1 and FSTL1 expression was more up-regulated in SF subset 3 compared to the other two subgroups.\nConclusions: IRF1 was found to regulate the invasiveness of SFs by regulating FSTL1, which may influence the disease progression of RA.", "claims": [{"id": "claim-method", "statement": "Then, DESeq2 [24] was used to perform differential expression analysis on the constructed pseudobulk transcript data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35572839", "locator": "sections[6] \"2.4. Differential Expression Analysis\" paragraph 2", "quote": "Then, DESeq2 [24] was used to perform differential expression analysis on the constructed pseudobulk transcript data."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data for this study were obtained from the GSE109449 dataset of the GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35572839", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "The data for this study were obtained from the GSE109449 dataset of the GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "IRF1 was found to regulate the invasiveness of SFs by regulating FSTL1, which may influence the disease progression of RA.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35572839", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "IRF1 was found to regulate the invasiveness of SFs by regulating FSTL1, which may influence the disease progression of RA."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "IRF1 was found to regulate the invasiveness of SFs by regulating FSTL1, which may influence the disease progression of RA.", "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:35572839"], "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:GSE109449"], "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:GSE109449"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35572839", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/1169614", "sha256": 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