Yanjun Lin1,2,3,4, Xiu Yao1,5, Mingdong Yan1,4,6, Lin Zhou4,7, Wenxiu Huang4,7, Yanjun Xiao4,7, Dong Wu4,7, Jiang Chen4,7,8. 1. Fujian Key Laboratory of Oral Diseases, Fujian Medical University, Fuzhou, Fujian, China. 2. Fujian Provincial Engineering Research Center of Oral Biomaterial, Fujian Medical University, Fuzhou, Fujian, China. 3. Stomatological Key Lab of Fujian College and University, Fuzhou, Fujian, China. 4. Department of Oral Implantology, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian, China. 5. Research Center of Dental Esthetics and Biomechanics, Fujian Medical University, Fuzhou, Fujian, China. 6. Laboratory of Oral Tissue Engineering, Fujian Medical University, Fuzhou, Fujian, China. 7. Research Center of Dental and Craniofacial Implants, Fujian Medical University, Fuzhou, Fujian, China. 8. Institute of Stomatology, Fujian Medical University, Fuzhou, Fujian, China.
Abstract
OBJECTIVE: The treatment of patients with primary Sjögren's syndrome is a clinical challenge. Gene expression profile analysis and comprehensive network methods for complex diseases can provide insight into molecular characteristics in the clinical context. MATERIALS AND METHODS: We downloaded gene expression datasets from the Gene Expression Omnibus (GEO) database. We screened differentially expressed genes (DEG) between the pSS patients and the controls by the robust rank aggregation (RRA) method. We explored DEGs' potential function using gene function annotation and PPI network analysis. RESULTS: GSE23117, GSE40611, GSE80805, and GSE127952 were included, including 38 patients and 30 controls. The RRA integrated analysis determined 294 significant DEGs (241 upregulated and 53 downregulated), and the most significant gene aberrantly expressed in SS was CXCL9 (p = 6.39E-15), followed by CXCL13 (p = 1.53E-13). Immune response (GO:0006955; p = 4.29E-32) was the most significantly enriched biological process in GO (gene ontology) analysis. KEGG pathway enrichment analysis showed that cytokine-cytokine receptor interaction (hsa04060; p = 6.46E-10) and chemokine signaling pathway (hsa04062; p = 9.54E-09) were significantly enriched. We defined PTPRC, CD86, and LCP2 as the hub genes based on the PPI results. CONCLUSION: Our integrated analysis identified gene signatures and helped understand molecular changes in pSS.
OBJECTIVE: The treatment of patients with primary Sjögren's syndrome is a clinical challenge. Gene expression profile analysis and comprehensive network methods for complex diseases can provide insight into molecular characteristics in the clinical context. MATERIALS AND METHODS: We downloaded gene expression datasets from the Gene Expression Omnibus (GEO) database. We screened differentially expressed genes (DEG) between the pSS patients and the controls by the robust rank aggregation (RRA) method. We explored DEGs' potential function using gene function annotation and PPI network analysis. RESULTS: GSE23117, GSE40611, GSE80805, and GSE127952 were included, including 38 patients and 30 controls. The RRA integrated analysis determined 294 significant DEGs (241 upregulated and 53 downregulated), and the most significant gene aberrantly expressed in SS was CXCL9 (p = 6.39E-15), followed by CXCL13 (p = 1.53E-13). Immune response (GO:0006955; p = 4.29E-32) was the most significantly enriched biological process in GO (gene ontology) analysis. KEGG pathway enrichment analysis showed that cytokine-cytokine receptor interaction (hsa04060; p = 6.46E-10) and chemokine signaling pathway (hsa04062; p = 9.54E-09) were significantly enriched. We defined PTPRC, CD86, and LCP2 as the hub genes based on the PPI results. CONCLUSION: Our integrated analysis identified gene signatures and helped understand molecular changes in pSS.