背景:几十年来,坏死性软组织感染(NSTI)的基本治疗策略保持不变,主要依靠积极的手术切除受感染的组织,广谱抗生素,和支持性重症监护。一种已被提出作为改善患者预后的辅助措施的治疗策略是高压氧(HBO2)治疗。HBO2治疗与几种免疫调节作用有关;然而,由于这种疾病的急性危及生命的性质,调查这些影响是复杂的,治疗效果的代谢和细胞稳态依赖性变异性,以及患者特征和相关病原体的异质性。为了拥抱这种复杂性,我们旨在从基因表达水平探讨HBO2治疗NSTI患者的生物学机制。
方法:我们对前瞻性收集的数据进行了观察性队列研究,包括因NSTI入住重症监护病房(ICU)的85名患者。所有患者均接受一次或两次HBO2治疗,并在干预前后采集了一份血液样本。从血液样品中提取总RNA,用rRNA去除纯化mRNA,然后是全转录组RNA测序,靶向测序深度为20百万个读数。拟合了差异表达基因(DEGs)的模型,并且利用GO(基因本体论)和KEGG(基因和基因组的京都百科全书)富集分析来预测所获得的基因集合的功能方面。所有分析都用FDR进行多次测试校正。
结果:经过连续的质量控制步骤,最终的160个生物学重复被包括在本研究中。我们发现394个蛋白质编码基因在FDR<0.01的两种条件下显著为DEGs,其中205个被上调,189个被下调。这些DEGs的富集分析揭示了生物过程中的20个GO术语和12个KEGG途径,这些途径在上调的DEGs中被显著地过度表达。其中术语“适应性免疫应答”(GO:0002250)(FDR=9.88E-13)和“T细胞受体信号通路”(hsa04660)(FDR=1.20E-07)最显著。在下调的DEGs中,两个生物过程显著富集,其中GO术语“凋亡过程”(GO:0006915)最显著(FDR=0.001),其次是“辅助性T细胞1细胞因子产生的正调节”(GO:2000556),和“NF-κB信号通路”(hsa04064)是唯一显著过度表达的KEGG通路(FDR=0.001)。
结论:当对因NSTI引起的免疫反应失调和全身炎症的患者进行一到两次HBO2治疗时,在干预过程中调节的重要基因参与T辅助细胞的激活和疾病诱导的高度炎症通路NF-κB的下调,这与促炎因子的mRNA水平降低有关。
背景:在INFECT研究期间收集了生物材料,在ClinicalTrials.gov(NCT01790698)注册。
BACKGROUND: For decades, the basic treatment strategies of necrotizing soft tissue infections (NSTI) have remained unchanged, primarily relying on aggressive surgical removal of infected tissue, broad-spectrum antibiotics, and supportive intensive care. One treatment strategy that has been proposed as an adjunctive measure to improve patient outcomes is hyperbaric oxygen (HBO2) treatment. HBO2 treatment has been linked to several immune modulatory effects; however, investigating these effects is complicated due to the disease\'s acute life-threatening nature, metabolic and cell homeostasis dependent variability in treatment effects, and heterogeneity with respect to both patient characteristics and involved pathogens. To embrace this complexity, we aimed to explore the underlying biological mechanisms of HBO2 treatment in patients with NSTI on the gene expression level.
METHODS: We conducted an observational cohort study on prospective collected data, including 85 patients admitted to the intensive care unit (ICU) for NSTI. All patients were treated with one or two HBO2 treatments and had one blood sample taken before and after the intervention. Total RNAs from blood samples were extracted and mRNA purified with rRNA depletion, followed by whole-transcriptome RNA sequencing with a targeted sequencing depth of 20 million reads. A model for differentially expressed genes (DEGs) was fitted, and the functional aspects of the obtained set of genes was predicted with GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of genes and Genomes) enrichment analyses. All analyses were corrected for multiple testing with FDR.
RESULTS: After sequential steps of quality control, a final of 160 biological replicates were included in the present study. We found 394 protein coding genes that were significantly DEGs between the two conditions with FDR < 0.01, of which 205 were upregulated and 189 were downregulated. The enrichment analysis of these DEGs revealed 20 GO terms in biological processes and 12 KEGG pathways that were significantly overrepresented in the upregulated DEGs, of which the term; \"adaptive immune response\" (GO:0002250) (FDR = 9.88E-13) and \"T cell receptor signaling pathway\" (hsa04660) (FDR = 1.20E-07) were the most significant. Among the downregulated DEGs two biological processes were significantly enriched, of which the GO term \"apoptotic process\" (GO:0006915) was the most significant (FDR = 0.001), followed by \"Positive regulation of T helper 1 cell cytokine production\" (GO:2000556), and \"NF-kappa B signaling pathway\" (hsa04064) was the only KEGG pathway that was significantly overrepresented (FDR = 0.001).
CONCLUSIONS: When one or two sessions of HBO2 treatment were administered to patients with a dysregulated immune response and systemic inflammation due to NSTI, the important genes that were regulated during the intervention were involved in activation of T helper cells and downregulation of the disease-induced highly inflammatory pathway NF-κB, which was associated with a decrease in the mRNA level of pro-inflammatory factors.
BACKGROUND: Biological material was collected during the INFECT study, registered at ClinicalTrials.gov (NCT01790698).