A single-cell RNA-seq dataset of synovial fluid from rheumatoid arthritis treated with TNF-α/JAK inhibitor

• Published in: Scientific data Vol. 12; no. 1; pp. 977 - 7
• Main Authors: He, Chenjia, Ren, Zhixiang, Xia, Xuyang, Xue, Zhinan, Zhang, Feng, Qian, Maoxiang, Shu, Yang, Yin, Geng, Xie, Qibing, Xu, Heng
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 10.06.2025; Nature Publishing Group; Nature Portfolio
• Subjects: 631/250/38; 692/699/249/1313/498; Adalimumab - therapeutic use; Arthritis, Rheumatoid - drug therapy; Arthritis, Rheumatoid - genetics; Cancer therapies; Data Descriptor; Datasets; Epigenetics; Genomics; Hospitals; Humanities and Social Sciences; Humans; Immunology; Inflammatory diseases; Janus Kinase Inhibitors - therapeutic use; Laboratories; Monoclonal antibodies; multidisciplinary; Pathogenesis; Patients; Piperidines - therapeutic use; Precision medicine; Pyrimidines - therapeutic use; Quality control; Rheumatoid arthritis; Rheumatology; RNA-Seq; Science; Science (multidisciplinary); Sequence Analysis, RNA; Single-Cell Analysis; Single-Cell Gene Expression Analysis; Surgery; Synovial Fluid; Therapeutic targets; Tumor Necrosis Factor-alpha - antagonists & inhibitors; Tumor necrosis factor-α
• ISSN: 2052-4463; 2052-4463
• DOI: 10.1038/s41597-025-05339-4

Although multiple single-cell RNA sequencing (scRNA-seq) based studies have explored rheumatoid arthritis (RA), most have focused on synovial tissue, limiting the ability to perform paired pre- and post-treatment comparisons and to elucidate dynamic changes. Moreover, the single-cell impact of TNF-α and JAK inhibitors on RA remains poorly understood, hindering effects toward precision medicine for RA. Here, we present a comprehensive scRNA-seq analysis of synovial fluid samples of RA patients treated with tofacitinib or adalimumab, both pre- and post-treatment. Following stringent quality control, we analyzed 100,387 high-quality cells, providing an in-depth characterization of cell composition, molecular signaling pathways, and functional properties. This rich dataset offers a valuable resource to address diverse research questions, from uncovering the mechanisms of action of TNF-α and JAK inhibitors, to identifying novel therapeutic targets for RA, and advancing our understanding of the pathogenesis of inflammatory diseases.