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The heterogeneity of the disease can be investigated via single-cell RNA sequencing (scRNA-seq) for its gap in the literature. Firstly, five types of immune cells (plasma cells, naive CD4 T cells, memory-activated CD4 T cells, eosinophils, and neutrophils) were significantly different between normal control (NC) and JIA samples. WGCNA was performed to identify genes that exhibited the highest correlation to differential immune cells. Then, 168 differentially expressed immune cell-related genes (DE-ICRGs) were identified by overlapping 13,706 genes identified by WGCNA and 286 differentially expressed genes (DEGs) between JIA and NC specimens. Next, four key genes, namely SOCS3, JUN, CLEC4C, and NFKBIA, were identified by a protein\u2013protein interaction (PPI) network and three machine learning algorithms. The results of functional enrichment revealed that SOCS3, JUN, and NFKBIA were all associated with hallmark TNF-\u03b1 signaling via NF-\u03baB. In addition, cells in JIA samples were clustered into four groups (B cell, monocyte, NK cell, and T cell groups) by single-cell data analysis. CLEC4C and JUN exhibited the highest level of expression in B cells; NFKBIA and SOCS3 exhibited the highest level of expression in monocytes. Finally, real-time quantitative PCR (RT-qPCR) revealed that the expression of three key genes was consistent with that determined by differential analysis. Our study revealed four key genes with prognostic value for JIA. Our findings could have potential implications for JIA treatment and investigation.<\/jats:p>","DOI":"10.3390\/ijms241310619","type":"journal-article","created":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T01:42:32Z","timestamp":1687743752000},"page":"10619","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Immune Cell-Related Genes in Juvenile Idiopathic Arthritis Identified Using Transcriptomic and Single-Cell Sequencing Data"],"prefix":"10.3390","volume":"24","author":[{"given":"Wenbo","family":"Zhang","sequence":"first","affiliation":[{"name":"The Joint Center for Infection and Immunity, Guangzhou Institute of Pediatrics, Guangzhou Women and Children\u2019s Medical Center, Guangzhou 510623, China"},{"name":"The Joint Center for Infection and Immunity, CAS Key Laboratory of Molecular Virology & Immunology, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510006, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhe","family":"Cai","sequence":"additional","affiliation":[{"name":"Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University, Guangzhou 510623, China"},{"name":"Guangzhou Institute of Pediatrics, Guangzhou Women and Children\u2019s Medical Center, Guangzhou 510623, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dandan","family":"Liang","sequence":"additional","affiliation":[{"name":"The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510006, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaochan","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University, Guangzhou 510623, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ping","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University, Guangzhou 510623, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayi","family":"Shan","sequence":"additional","affiliation":[{"name":"The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510006, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4634-4661","authenticated-orcid":false,"given":"Guangxun","family":"Meng","sequence":"additional","affiliation":[{"name":"The Joint Center for Infection and Immunity, CAS Key Laboratory of Molecular Virology & Immunology, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, University of Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huasong","family":"Zeng","sequence":"additional","affiliation":[{"name":"The Joint Center for Infection and Immunity, Guangzhou Institute of Pediatrics, Guangzhou Women and Children\u2019s Medical Center, Guangzhou 510623, China"},{"name":"Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children\u2019s Medical Center, Guangzhou Medical University, Guangzhou 510623, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,6,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1038\/s41572-021-00332-8","article-title":"Juvenile idiopathic arthritis","volume":"8","author":"Martini","year":"2022","journal-title":"Nat. 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