Table_6_The Peripheral Blood Transcriptome Is Correlated With PET Measures of Lung Inflammation During Successful Tuberculosis Treatment.xlsx

Pulmonary tuberculosis (PTB) is characterized by lung granulomas, inflammation and tissue destruction. Here we used within-subject peripheral blood gene expression over time to correlate with the within-subject lung metabolic activity, as measured by positron emission tomography (PET) to identify biological processes and pathways underlying overall resolution of lung inflammation. We used next-generation RNA sequencing and [18F]FDG PET-CT data, collected at diagnosis, week 4, and week 24, from 75 successfully cured PTB patients, with the [18F]FDG activity as a surrogate for lung inflammation. Our linear mixed-effects models required that for each individual the slope of the line of [18F]FDG data in the outcome and the slope of the peripheral blood transcript expression data correlate, i.e., the slopes of the outcome and explanatory variables had to be similar. Of 10,295 genes that changed as a function of time, we identified 639 genes whose expression profiles correlated with decreasing [18F]FDG uptake levels in the lungs. Gene enrichment over-representation analysis revealed that numerous biological processes were significantly enriched in the 639 genes, including several well known in TB transcriptomics such as platelet degranulation and response to interferon gamma, thus validating our novel approach. Others not previously associated with TB pathobiology included smooth muscle contraction, a set of pathways related to mitochondrial function and cell death, as well as a set of pathways connecting transcription, translation and vesicle formation. We observed up-regulation in genes associated with B cells, and down-regulation in genes associated with platelet activation. We found 254 transcription factor binding sites to be enriched among the 639 gene promoters. In conclusion, we demonstrated that of the 10,295 gene expression changes in peripheral blood, only a subset of 639 genes correlated with inflammation in the lungs, and the enriched pathways provide a description of the biology of resolution of lung inflammation as detectable in peripheral blood. Surprisingly, resolution of PTB inflammation is positively correlated with smooth muscle contraction and, extending our previous observation on mitochondrial genes, shows the presence of mitochondrial stress. We focused on pathway analysis which can enable therapeutic target discovery and potential modulation of the host response to TB.

肺结核（Pulmonary tuberculosis, PTB）以肺部肉芽肿、炎症及组织损伤为核心病理特征。本研究基于受试者自身的外周血基因表达时序数据，与通过正电子发射断层扫描（positron emission tomography, PET）检测的肺部代谢活性开展关联分析，旨在解析驱动肺部炎症完全消退的生物学过程与分子通路。本研究纳入75例经规范治疗后成功痊愈的PTB患者，分别在确诊时、治疗第4周及第24周三个时间点采集其下一代RNA测序（next-generation RNA sequencing）数据与[18F]FDG PET-CT影像数据，并以[18F]FDG摄取活性作为肺部炎症水平的替代检测指标。本研究所采用的线性混合效应模型设定如下：对于每名受试者，结局指标中[18F]FDG数据的变化斜率与外周血转录本表达数据的变化斜率需具备统计学相关性，即二者的变化趋势需趋于一致。在10295个随时间表达水平发生显著变化的基因中，本研究筛选得到639个基因，其表达谱与肺部[18F]FDG摄取水平的降低呈显著正相关。基因富集过表征分析结果显示，该639个基因显著富集于多种生物学过程，其中包括结核转录组学研究中已被广泛验证的血小板脱颗粒、干扰素γ应答等经典通路，由此证实了本研究分析方法的科学性与创新性。此外，本研究还发现了一批此前未被报道与结核病理生物学相关的生物学过程，包括平滑肌收缩、一系列与线粒体功能及细胞死亡相关的通路，以及连接转录、翻译与囊泡形成的调控通路集合。本研究观察到，与B细胞活化相关的基因呈现表达上调趋势，而与血小板活化相关的基因则呈现表达下调趋势。进一步分析显示，在该639个基因的启动子区域中，共富集得到254个转录因子结合位点。综上，本研究证实：在外周血的10295个时序变化基因中，仅有639个基因与肺部炎症水平存在显著关联；上述富集通路系统阐明了可通过外周血检测到的肺部炎症消退相关生物学机制。值得注意的是，PTB肺部炎症的消退进程与平滑肌收缩呈正相关；结合本团队此前关于线粒体基因的研究发现，该结果提示线粒体应激反应参与了肺部炎症的消退过程。本研究重点聚焦于通路分析，以期为结核治疗靶点的发掘以及宿主抗结核应答的精准调控提供理论支撑与研究方向。