The aim of present study was to find genetic pathways activated during infection with bacterial meningitis (BM) and potentially influencing the course of the infection using genome-wide RNA expression profiling combined with pathway analysis and functional annotation of the differential transcription. We analyzed 21 patients with BM hospitalized in 2008. The control group consisted of 18 healthy subjects. The RNA was extracted from whole blood, globin mRNA was depleted and gene expression profiling was performed using GeneChip Human Gene 1.0 ST Arrays which can assess the transcription of 28,869 genes. Gene expression profile data were analyzed using Bioconductor packages and Bayesian modeling. Functional annotation of the enriched gene sets was used to define the altered genetic networks. We also analyzed whether gene expression profiles depend on the clinical course and outcome. In order to verify the microarray results, the expression levels of ten functionally relevant genes with high statistical significance (CD177, IL1R2, IL18R1, IL18RAP, OLFM4, TLR5, CPA3, FCER1A, IL5RA, IL7R) were confirmed by quantitative real-time (qRT) PCR. There were 8569 genes displaying differential expression at a significance level of p 0.05. Following False Discovery Rate (FDR) correction, a total of 5500 genes remained significant at a p value of 0.01. Quantitative RT-PCR confirmed the differential expression in the 10 selected genes. Functional annotation and network analysis indicated that most of the genes were related to activation of humoral and cellular immune responses (enrichment score 43). Those changes were found in both adults and in children with BM compared to the healthy controls. There was a strong influence of the specific type of pathogen underlying BM. This study demonstrates that there is a very strong activation of immune response at the transcriptional level during BM and that the type of pathogen influences this transcriptional activation.
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机译：本研究的目的是使用全基因组RNA表达谱分析，结合途径分析和差异转录功能注释，找出在细菌性脑膜炎（BM）感染期间激活的遗传途径，并可能影响感染过程。我们分析了2008年住院的21例BM患者。对照组由18名健康受试者组成。从全血中提取RNA，消耗珠蛋白mRNA，并使用可评估28,869个基因转录的GeneChip Human Gene 1.0 ST Arrays进行基因表达谱分析。使用Bioconductor软件包和贝叶斯模型分析基因表达谱数据。丰富的基因集的功能注释用于定义改变的遗传网络。我们还分析了基因表达谱是否取决于临床过程和结果。为了验证微阵列结果，通过定量实时（qRT）确认了十个具有统计学意义的功能相关基因（CD177，IL1R2，IL18R1，IL18RAP，OLFM4，TLR5，CPA3，FCER1A，IL5RA，IL7R）的表达水平）PCR。有8569个基因显示差异表达，显着性水平为p <0.05。在错误发现率（FDR）校正之后，总共5500个基因保持显着性，p值<0.01。定量RT-PCR证实了10个选定基因的差异表达。功能注释和网络分析表明，大多数基因与体液和细胞免疫应答的激活有关（富集得分43）。与健康对照组相比，在成年人和患有BM的儿童中均发现了这些变化。 BM所致病原体的特定类型有很大影响。这项研究表明，在BM的转录水平上，免疫应答的激活非常强，病原体的类型会影响这种转录的激活。
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