Application Of Data Mining In Rheumatoid Arthritis

Part ?:Comparison of disease activity indicators for rheumatoid arthritis(RA)based on CREDIT databaseObjective:To compare the consistency of disease activity indicators among RA patients in China by using CREDIT database,and to try to determine the disease activity threshold "suitable for China".Methods:Baseline data of all patients who met the requirements of core data in 24 months(October 2016-October 2018)since the establishment of CREDIT database were analyzed.(1)The correlation among four disease activity indicators(DAS28-ESR,DAS28-CRP,SDAI and CDAI)was analyzed.(2)Consistency among four indicators:a.cross table,b.quadratic weighted kappa coefficient,c.Bland-Altman plot.(3)Taking SDAI<3.3 in remission period as the standard,the threshold values of DAS28-ESR,DAS28-CRP and CDAI were calculated by ROC curve method.Results:A total of 30501 RA patients were enrolled,of whom 80.46%were women.Most patients were in moderate to severe active state.There is a high correlation among the four indicators,and the weighted Kappa value among the indicators is also high.In Bland-Altman plot,DAS28-ESR was significantly higher than DAS28-CRP,and the absolute difference between DAS28-ESR and DAS28-CRP was more than 1.2 in 3079 cases(10.09%).Nearly 30%of patients were divided into different disease activity groups according to different activity indices in the cross-tabular comparison between the two groups.With SDAI?3.3 as the criterion of remission period,the threshold values of DAS28-ESR,DAS28-CRP and CDAI were re-determined by ROC curve method,which were 3.06,2.37 and 3.2,respectively.Conclusion:Although there is a high correlation and a high weighted Kappa value among the four disease activity indices in RA patients in China,there are significant inconsistencies among the four disease activity indices.Four disease activity indices cannot be substituted for each other.Part ?:Bioinformatics analysis of rheumatoid arthritis related genesObjective:Rheumatoid arthritis(RA)is a common autoimmune disease.The aim of this study is to analyze the genes and signaling pathways closely related to the pathogenesis of RA by bioinformatics.Methods:We downloaded the complete gene chip expression information of GSE17755 Series in GEO database.The software R was used to analyze differentially expressed genes by limma package and weighted gene co-expression network analysis(WGCNA).Method I.Differential genes(DEGs)were enriched on DAVID website firstly,then protein-protein interaction network(PPI)was constructed by STRING software,and key genes were identified by constructing subnetwork of Cytoscape.Method II.DEGs identified several modules related to RA by WGCNA method;enriched the genes in the modules with the highest correlation;and finally constructed a gene co-expression network related to RA through Cytoscape,and identified key genes using a plug-in:CytoHubba.Results:In method ?,469 DEGs were obtained,including 229 up-regulated genes and 240 down-regulated genes.Gene ontology(GO)analysis suggests that up-regulated genes are mainly concentrated in inflammatory response,while down-regulated genes are mainly related to intercellular adhesion and transport.KEGG signaling pathway analysis suggests that down-regulated genes are mainly related to the signal pathway of antigen presentation and expression,while up-regulated genes are not significantly related to the signal pathway after enrichment.Down-regulated DEGs constructed two subnetworks through STRING,finally HSPA8 and RPL3 were identified as the most important key genes.Method II:3666 DEGs and 8 modules were obtained.Among them,the module with the highest correlation with RA contains 1044 genes.These DEGs were enriched with GO analysis,which indicated that DEGs were mainly related to inflammatory response,Toll-like receptor(TLR)signaling pathway and B cell receptor activation signaling pathway.Ten key genes including PIGL,PRKAA1 and MRPS10 were identified.Conclusion:(1)HSPA8,RPL3 and their closely related genes may play an important role in the occurrence and progression of RA,and these genes may become new targets for RA therapy in the future.(2)Inflammatory response,Toll-like receptor(TLR)signaling pathway and B cell receptor activation signaling pathway may play a key role in the pathogenesis of RA;PIGL,PRKAA1 and MRPS10 may become new targets for RA research.Part?:Study on the Secretion of IL-10 by B Cell in Rheumatoid ArthritisObjective:To study the expression of B cell,regulatory B cells(Bregs),BAFF and its receptors and Toll-like receptors(TLRs)in rheumatoid arthritis(RA)and their relationship with disease activity,and to further explore the function and regulatory factors for B cell secreting IL-10 in RA.Methods:40 cases of RA and 20 healthy controls were selected.The levels of BAFF in peripheral serum were measured by ELISA.Peripheral blood mononuclear cells(PBMCs)were isolated from 20ml venous blood.The percentage of B cells,Bregs(CD24hiCD38hi,CD24hiCD27+)and the expression of TLR7,TLR9 and BAFF related receptors(TACI,BAFFR,BCMA)in B cells were detected by flow cytometry.The expression of TLR7 and TLR9 in B cells were measured by fluorescence quantitative PCR at the level of mRNA.Then,30 cases of RA and 15 healthy controls were selected.The levels of IL-10 in serum were measured by ELISA.Negative selection of B cells by magnetic beads in PBMCs was treated with TLR9(CPG-ODN)or BAFF alone,combined with TLR9(CPG-ODN)and BAFF stimulation.The expression of IL-10 was detected by ELISA and flow cytometry,respectively.Results:(1)Compared with healthy control group,BAFF in peripheral serum of RA increased significantly.(2)Compared with healthy controls,the proportion of B cell and Bregs in RA patients was not different.The expression of TLR9 and TACI in B cells increased significantly,but there was no significant difference among TLR7,BAFFR and BCMA.(3)According to DAS28,RA patients was divided into medium and high disease activity group(DAS28>3.2),remission and low disease activity group(DAS28<3.2),TLR9-MFI increased significantly in medium and high disease activity group.(4)IL-10 was low expressed in serum and B cells without stimulation,but the stimulation effect of BAFF alone was not obvious,while TLR9 and TLR9+BAFF had obvious stimulation effect on IL-10 secretion by B cells.Compared with healthy controls,IL-10 secretion by B cells in RA patients was significantly reduced,and the expression of IL-10 was negatively correlated with DAS28-ESR.The results of ELISA and flow cytometry were similar.Conclusion:Compared with healthy controls,the expression of B cell and regulatory B cells in RA patients is not significantly different,but the secretion of IL-10 is significantly reduced,suggesting that the function of regulatory B cells in RA may be impaired.And the stimulation of CpG-ODN 2006 at the appropriate concentration can promote the secretion of IL-10 by B cells,so it may become a new target for the treatment of RA.However,the effect of BAFF on the secretion of IL-10 by B cells and the regulation of BAFF on B cells via TLR9 pathway were not found in this study.