Analysis of the lung transcriptome in Mycobacterium tuberculosis-infected mice reveals major differences in immune response pathways between TB-susceptible and resistant hosts

Using whole genome microarrays, we compared changes in gene expression patterns in the lungs of TB-resistant A/Sn and TB-susceptible I/St mice at day 14 following infection with Mycobacterium tuberculosis H37Rv. Analyses of differentially expressed genes for representation of gene ontology terms and activation of regulatory pathways revealed interstrain differences in antigen presentation, NK, T and B cell activation pathways. In general, resistant A/Sn mice exhibited a more complex pattern and stronger activation of host defense pathways compared to the TB-susceptible I/St mouse strain. In addition, in I/St mice elevated activation of genes involved in neutrophil response was observed and confirmed by quantitative RT-PCR and histopathology. Furthermore, a specific post infection upregulation of cysteine protease inhibitors was found in susceptible I/St mice. To monitor the global transcriptome patterns in the two mouse strains, gene expression was assessed using Agilent 4 x44K whole genome microarrays. Genes that changed their expression level at least two-fold compared to non-infected controls with a p-value of 0.1 were considered as differentially expressed genes (DEG).本研究采用全基因组微阵列（whole genome microarrays），对比分析了感染结核分枝杆菌H37Rv（Mycobacterium tuberculosis H37Rv）后第14天，抗结核A/Sn小鼠与结核易感I/St小鼠肺组织的基因表达模式变化。通过对差异表达基因开展基因本体（Gene Ontology）术语富集分析及调控通路激活特征分析，发现两种品系小鼠在抗原呈递、自然杀伤（NK）细胞、T细胞及B细胞激活通路上存在品系间差异。总体而言，相较于结核易感的I/St小鼠品系，抗结核A/Sn小鼠的宿主防御通路激活模式更为复杂，激活强度也更强。此外，经定量逆转录聚合酶链反应（quantitative RT-PCR）及组织病理学（histopathology）验证，I/St小鼠中参与中性粒细胞应答的基因激活水平显著升高。进一步研究发现，易感品系I/St小鼠在感染后会特异性上调半胱氨酸蛋白酶抑制剂（cysteine protease inhibitors）的基因表达。为检测两种小鼠品系的全局转录组（transcriptome）表达谱特征，本研究采用安捷伦（Agilent）4×44K全基因组微阵列进行基因表达检测。最终将与未感染对照组相比表达水平变化幅度至少达2倍、且p值为0.1的基因，认定为差异表达基因（DEG）。