Blood transcriptomics to characterize key biological pathways and identify biomarkers for predicting mortality in melioidosis

Melioidosis is an often lethal tropical disease caused by the Gram-negative bacillus, <i>Burkholderia pseudomallei</i>. The study objective was to characterize transcriptomes in melioidosis patients and identify genes associated with outcome. Whole blood RNA-seq was performed in a discovery set of 29 melioidosis patients and 3 healthy controls. Transcriptomic profiles of patients who did not survive to 28 days were compared with patients who survived and healthy controls, showing 65 genes were significantly up-regulated and 218 were down-regulated in non-survivors compared to survivors. Up-regulated genes were involved in myeloid leukocyte activation, Toll-like receptor cascades and reactive oxygen species metabolic processes. Down-regulated genes were hematopoietic cell lineage, adaptive immune system and lymphocyte activation pathways. RT-qPCR was performed for 28 genes in a validation set of 60 melioidosis patients and 20 healthy controls, confirming differential expression. <i>IL1R2, GAS7, S100A9, IRAK3,</i> and <i>NFKBIA</i> were significantly higher in non-survivors compared with survivors (<i>P</i> &lt; 0.005) and healthy controls (<i>P</i> &lt; 0.0001). The AUROCC of these genes for mortality discrimination ranged from 0.80-0.88. In survivors, expression of <i>IL1R2</i>, <i>S100A9</i> and <i>IRAK3</i> genes decreased significantly over 28 days (<i>P</i> &lt; 0.05). These findings augment our understanding of this severe infection, showing expression levels of specific genes are potential biomarkers to predict melioidosis outcomes.

类鼻疽（Melioidosis）是一种常可致死的热带感染性疾病，由革兰氏阴性杆菌假鼻疽伯克霍尔德菌（Burkholderia pseudomallei）引发。本研究旨在解析类鼻疽患者的转录组特征，并筛选与疾病转归相关的基因。研究首先对29例类鼻疽患者与3名健康对照者的全血样本开展RNA测序（RNA-seq），构建发现集队列。随后将28天随访期内未存活患者的转录组谱与存活患者及健康对照进行对比，结果显示，相较于存活患者，未存活患者体内共有65个基因显著上调、218个基因显著下调。上调基因主要富集于髓系白细胞活化、Toll样受体级联反应以及活性氧代谢过程；下调基因则涉及造血细胞谱系、适应性免疫系统与淋巴细胞活化通路。为验证上述结果，本研究在包含60例类鼻疽患者与20名健康对照者的验证集队列中，针对28个基因开展了实时定量聚合酶链反应（RT-qPCR），证实了其差异表达特征。与存活患者及健康对照者相比，未存活患者体内IL1R2、GAS7、S100A9、IRAK3及NFKBIA的表达水平显著升高（相较于存活患者P<0.005，相较于健康对照P<0.0001）。上述基因用于区分患者死亡率的受试者工作特征曲线下面积（AUROCC）介于0.80至0.88之间。在存活患者中，IL1R2、S100A9及IRAK3的表达水平在28天随访期内显著降低（P<0.05）。本研究结果加深了学界对这类重症感染的认知，提示特定基因的表达水平可作为预测类鼻疽疾病转归的潜在生物标志物。