生物信息学分析方法探讨类风湿关节炎患者滑膜病变中的免疫细胞浸润

Bioinformatics analysis to investigate immune cell infiltration in synovial lesions of rheumatoid arthritis patients

目的探索RA滑膜病变中的免疫浸润细胞,为RA的机制及治疗研究提供新的研究方向及治疗靶点。方法从基因表达综合数据库(GEO)(http://www.ncbi.nlm.nih.gov/geo)下载GSE77298、GSE55457和GSE1919三个基因表达数据集,Perl进行数据合并,R的"limma"进行批次矫正。在R中用"CIBERSORT"软件通过"e1071""parallel"和"preprocessCore"3个包获得22种免疫细胞对应RA滑膜组织样本和正常滑膜组织样本的表达矩阵。Perl筛选免疫细胞矩阵中P<0.05的样本。R的"barplot"函数分析22种免疫细胞在P<0.05的样本中的含量百分比。R的"pheatmap"包可视化热图,R的"corrplot"包绘制相关性热图。R的"vioplot"包通过wilcox检验绘制差异小提琴图。结果免疫细胞浸润分析结果表明,在P<0.05的RA滑膜组织样本和正常滑膜组织样本中,初始B细胞和未活化的自然杀伤细胞在RA滑膜组织中低表达,浆细胞、未活化的肥大细胞、M1巨噬细胞、记忆性B细胞和调节性T细胞在RA滑膜组织中高表达。研究还发现在同一样本中,活化的自然杀伤细胞与中性粒细胞的相关系数(r=0.91)最高,呈正相关,两者具有协同效应。在同一样本中,M0巨噬细胞和浆细胞的相关系数(r=-0.88)最低,呈负相关,两者具有拮抗作用。结论本研究发现的RA滑膜病变中的免疫浸润细胞为RA的机制研究及治疗研究提供了一定的理论依据和研究方向。

Objective To explore the immune infiltration cells in rheumatoid arthritis(RA)synovial lesions,and to provide new research directions and therapeutic targets for the pathogenesis and treatment of RA.Methods The three gene expression data sets GSE77298,GSE55457 and GSE1919 were downloaded from gene expression omnibus(GEO)(http://www.ncbi.nlm.nih.gov/geo),and the data were merged with Perl.The"limma"package was used to adjust batch differences.In R,"CIBERSORT"software was used to obtain the expression matrix of 22 kinds of immune cells corresponding to RA synovial tissue samples and normal synovial tissue samples were analyzed with the three packages of"e1071","parallel"and"preprocessCore".Perl was used to screen samples with P<0.05 in the immune cell matrix.R's"barplot"function was analyzed by the percentage of 22 immune cells in samples with P<0.05.The"pheatmap"package of R was used to visualize heatmaps,and"corrplot"package was used to draw correlation heatmaps.The"vioplot"package of R was used to draw violin plots of differences via the wilcox test.Results The results of immune cell infiltration analysis showed that in RA synovial tissue samples and normal synovial tissue samples at P<0.05,B cells naive and natural killer cells resting were under-expressed in RA synovial tissue,and plasma cells,mast cells resting,macrophages M1,B cells memory and T cells regulatory were highly expressed in RA synovial tissue.This study also found that in the same sample,the correlation coefficient between natural killer cells resting and neutrophils(r=0.91)was the highest,indicating synergistic effect between the two.In the same sample,the correlation coefficient between macrophages M0 and plasma cells(r=-0.88)was the lowest,indicating antagonistic effect between the two.Conclusion The immune infiltrating cells in RA synovial lesions discovered in this study provide a certain theoretical basis and research direction for the research on the disease mechanism and treatment of RA.