{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T06:45:40Z","timestamp":1782801940056,"version":"3.54.5"},"reference-count":28,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T00:00:00Z","timestamp":1782432000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease in which senescence-associated secretory phenotype (SASP)-related transcriptional programs may contribute to synovial inflammation and fibroblast activation. This study aimed to integrate bulk transcriptomic cohorts with the gene-expression component of a single-nucleus multimodal dataset to identify reproducible SASP-related candidate biomarkers and prioritize fibroblast-associated signals in RA. Methods: SASP-score correlation analysis, differential expression analysis, cross-cohort evaluation, logistic regression, gene set enrichment analysis, single-nucleus transcriptomic characterization, predicted regulatory network analysis, and RT-qPCR assessment were performed. GSE89408 was used as the discovery bulk transcriptomic cohort, GSE77298 as the external evaluation cohort, and GSE243917 as the single-nucleus gene-expression dataset. Results: Fibroblasts showed relatively high SASP-related transcriptional scores within the RA single-nucleus dataset. The cross-cohort evaluation retained RCAN1, IRF1, CFB, and TIMP1 as reproducibly elevated candidates. Among all 15 non-empty panels derived from these four genes, the RCAN1\/IRF1\/CFB panel achieved the highest five-fold cross-validated AUC in GSE89408 and tied for the highest external AUC in GSE77298. Adding TIMP1 did not improve the external AUC or the 95% confidence interval. Among the retained genes, CFB showed the strongest fibroblast-associated expression pattern and SASP-score correlation. The RT-qPCR analysis provided preliminary mRNA-level support for the increased expression of RCAN1, IRF1, and CFB in the RA-related cell samples. Conclusions: RCAN1, IRF1, and CFB form a reproducible SASP-related candidate panel in RA, with CFB prioritized as a fibroblast-associated marker. Further protein-level, functional, and controlled single-cell validation studies are required.<\/jats:p>","DOI":"10.3390\/genes17070736","type":"journal-article","created":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T05:58:04Z","timestamp":1782799084000},"page":"736","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated Bulk and Single-Cell Transcriptomic Analysis Identifies a Reproducible SASP-Related Three-Gene Panel and Prioritizes CFB as a Fibroblast-Associated Marker in Rheumatoid Arthritis"],"prefix":"10.3390","volume":"17","author":[{"given":"Jiang","family":"Zhang","sequence":"first","affiliation":[{"name":"Shenzhen University Health Science Center, Shenzhen University, Shenzhen 518060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming","family":"Li","sequence":"additional","affiliation":[{"name":"Shenzhen University Health Science Center, Shenzhen University, Shenzhen 518060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuancheng","family":"Jin","sequence":"additional","affiliation":[{"name":"Shenzhen University Health Science Center, Shenzhen University, Shenzhen 518060, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaojing","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Rehabilitation Medicine, Shenzhen University General Hospital, Shenzhen 518055, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,26]]},"reference":[{"key":"ref_1","first-page":"591","article-title":"Global epidemiology of rheumatoid arthritis","volume":"18","author":"Finckh","year":"2022","journal-title":"Nat. Rev. Rheumatol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"102400","DOI":"10.1016\/j.jaut.2019.102400","article-title":"The etiology of rheumatoid arthritis","volume":"110","author":"Scherer","year":"2020","journal-title":"J. Autoimmun."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1038\/s41580-024-00727-x","article-title":"The senescence-associated secretory phenotype and its physiological and pathological implications","volume":"25","author":"Wang","year":"2024","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/s12979-019-0169-4","article-title":"Senescent synovial fibroblasts accumulate prematurely in rheumatoid arthritis tissues and display an enhanced inflammatory phenotype","volume":"16","author":"Usategui","year":"2019","journal-title":"Immun. Ageing"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1038\/s41467-018-02892-y","article-title":"Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis","volume":"9","author":"Mizoguchi","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"4490","DOI":"10.4049\/jimmunol.1601988","article-title":"CD40L-Dependent Pathway Is Active at Various Stages of Rheumatoid Arthritis Disease Progression","volume":"198","author":"Guo","year":"2017","journal-title":"J. Immunol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1089\/hum.2015.127","article-title":"Disease-Regulated Gene Therapy with Anti-Inflammatory Interleukin-10 Under the Control of the CXCL10 Promoter for the Treatment of Rheumatoid Arthritis","volume":"27","author":"Broeren","year":"2016","journal-title":"Hum. Gene Ther."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2200","DOI":"10.1038\/s41588-023-01577-7","article-title":"Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability","volume":"55","author":"Gupta","year":"2023","journal-title":"Nat. Genet."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1158\/1535-7163.MCT-23-0738","article-title":"Prognostic Significance of SASP-Related Gene Signature of Radiation Therapy in Head and Neck Squamous Cell Carcinoma","volume":"23","author":"Lee","year":"2024","journal-title":"Mol. Cancer Ther."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1016\/j.cell.2020.03.008","article-title":"Senescence-Induced Vascular Remodeling Creates Therapeutic Vulnerabilities in Pancreas Cancer","volume":"181","author":"Ruscetti","year":"2020","journal-title":"Cell"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","article-title":"DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors","volume":"8","author":"McGinnis","year":"2019","journal-title":"Cell Syst."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1186\/s13075-022-02902-x","article-title":"Identification of HBEGF+ fibroblasts in the remission of rheumatoid arthritis by integrating single-cell RNA sequencing datasets and bulk RNA sequencing datasets","volume":"24","author":"Chen","year":"2022","journal-title":"Arthritis Res. Ther."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: An R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"Omics"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1038\/s41467-021-21246-9","article-title":"Inference and analysis of cell-cell communication using CellChat","volume":"12","author":"Jin","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nbt.2859","article-title":"The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells","volume":"32","author":"Trapnell","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1126\/science.aax0249","article-title":"Single-cell transcriptional diversity is a hallmark of developmental potential","volume":"367","author":"Gulati","year":"2020","journal-title":"Science"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1111\/j.0105-2896.2009.00859.x","article-title":"Fibroblast-like synoviocytes: Key effector cells in rheumatoid arthritis","volume":"233","author":"Bartok","year":"2010","journal-title":"Immunol. Rev."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1080\/07853890701477546","article-title":"Rheumatoid arthritis and the complement system","volume":"39","author":"Okroj","year":"2007","journal-title":"Ann. Med."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"102979","DOI":"10.1016\/j.jaut.2022.102979","article-title":"The complement system and human autoimmune diseases","volume":"137","author":"Coss","year":"2023","journal-title":"J. Autoimmun."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"R122","DOI":"10.1186\/ar4579","article-title":"Enhanced neutrophil extracellular trap generation in rheumatoid arthritis: Analysis of underlying signal transduction pathways and potential diagnostic utility","volume":"16","author":"Giaglis","year":"2014","journal-title":"Arthritis Res. Ther."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1038\/s41590-023-01527-9","article-title":"Drivers of heterogeneity in synovial fibroblasts in rheumatoid arthritis","volume":"24","author":"Smith","year":"2023","journal-title":"Nat. Immunol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"6998","DOI":"10.1007\/s12035-024-04634-2","article-title":"NF-\u03baB Signaling Pathway in Rheumatoid Arthritis: Mechanisms and Therapeutic Potential","volume":"62","author":"Liao","year":"2025","journal-title":"Mol. Neurobiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"108793","DOI":"10.1016\/j.clim.2021.108793","article-title":"Recent advances on signaling pathways and their inhibitors in rheumatoid arthritis","volume":"230","author":"Liu","year":"2021","journal-title":"Clin. Immunol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Shi, W., Zheng, Y., Luo, S., Li, X., Zhang, Y., Meng, X., Huang, C., and Li, J. (2021). METTL3 Promotes Activation and Inflammation of FLSs Through the NF-\u03baB Signaling Pathway in Rheumatoid Arthritis. Front. Med., 8.","DOI":"10.3389\/fmed.2021.607585"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.semarthrit.2020.10.008","article-title":"The Jak\/STAT pathway: A focus on pain in rheumatoid arthritis","volume":"51","author":"Simon","year":"2021","journal-title":"Semin. Arthritis Rheum."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/7\/736\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T06:14:50Z","timestamp":1782800090000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/7\/736"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,26]]},"references-count":28,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,7]]}},"alternative-id":["genes17070736"],"URL":"https:\/\/doi.org\/10.3390\/genes17070736","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,26]]}}}