A time-course microarray data analysis reveals consistent dysregulated genes and upstream microRNAs in autoantibody-mediated arthritis

• Main Authors: Xinwen Wang, Jie Bai, Zhen Jia, Yangjun Zhu, Jijun Liu, Kun Zhang, Dingjun Hao, Lisong Heng
• Format: Article
• Language: English
• Published: BMC 2017-12-01
• Series: Journal of Orthopaedic Surgery and Research
• Subjects: Arthritis; Differentially expressed genes; MicroRNA; Regulatory network
• Online Access: http://link.springer.com/article/10.1186/s13018-017-0674-0

Abstract Background The purpose of this study is to identify key genes and microRNAs (miRNAs) involved in autoantibody-mediated arthritis (AMA). Methods A time-course microarray data (ID: GSE27492) of peripheral blood leukocytes, ankle tissue, and synovial fluid from K/BxN mouse serum-transferred mice were downloaded from Gene Expression Omnibus. Those samples were collected at days 0, 1, 3, 7, 12, and 18 after serum injection. Limma of R was employed to identify differentially expressed genes (DEGs) in samples collected at days 1–18 compared with those collected at day 0. Consistent DEGs were obtained by taking the interaction of DEGs from different time points, followed by functional enrichment analysis. MiRNAs were screened out and constructed into regulatory network with DEGs using Cytoscape. Results In total, 17 consistent DEGs were obtained, including downregulated Ephx1 and upregulated AF251705, Adam8, Arg1, Basp1, Ccl2, Ccl7, Ccl9, Ccr2, Clec4a2, Clec4d, Cxcl1, Fabp5, Fcgr1, Gp49a, Il1rn, and Saa3. Those DEGs were associated with biological processes of immune response, inflammatory response, and defense response; chemokine signaling pathway; cytokine-cytokine receptor interaction; and NOD-like receptor signaling pathway. Additionally, 202 miRNAs were identified to have a regulatory effect on 9 of the 17 DEGs. Notably, miR-944, miR-374a, and miR374b were found to regulate the expression of Cxcl1, Ccl7, and Ccl2. Clec4d was targeted by 78 miRNAs. Conclusions Our study reveals that 17 DEGs and 202 miRNAs may be associated with autoimmune disorder in the progression of AMA, which could guide future researches.