Cell-free DNA epigenomics to track the dynamics of organ damage and immune exhaustion during sepsis

项目总结 败血症是美国医院最常见的死亡原因，也是 全球范围内的死亡人数，2017年造成1100万人死亡。脓毒症发病率的主要驱动因素和 死亡是免疫衰竭导致致命的继发感染和器官组织损伤 导致多器官衰竭。尽管这些过程在管理终极 对于脓毒症的结局，我们对其动力学和动力学的了解还不完全。因此，我们 提出一项双管齐下的努力，通过无血浆细胞改变我们关于脓毒症动力学的范式 DNA分析。具体地说，我们建议1)跟踪特定器官损伤的动力学，以及2)跟踪 脓毒症时T细胞耗竭的动态变化。我们将通过分析每天的血液样本来做到这一点 感染自重症监护室的败血症患者。在方法上，我们将实现 这些都是通过对无细胞DNA进行全基因组甲基化测序实现的。从生物信息学上讲，我们将 执行CIBERSORTx反卷积以描述和量化特定细胞/组织类型 不含浆细胞的DNA，从而使我们能够推断器官组织和T细胞受到损害 血液和组织来源的消耗水平。我们将在这里使用的方法是高度 考虑到最近的文献和我们自己的初步数据，这是创新的，但也是可行的。我们提议的工作将 利用无细胞DNA分析为丰富的脓毒症研究计划奠定基础 回答现场的主要问题，最终有可能提高患者的存活率 世界上最致命的疾病。

PROJECT SUMMARY Sepsis is the most frequent cause of death in United States hospitals, and the number one cause of death worldwide, responsible for 11 million deaths in 2017. Primary drivers of sepsis morbidity and mortality are immune exhaustion leading to deadly secondary infection, and organ tissue damage leading to multi-organ failure. Despite the critical importance of these processes in governing ultimate sepsis outcomes, we have an incomplete understanding of their kinetics and dynamics. We thus propose a two-pronged effort to shift our paradigm regarding sepsis dynamics through plasma cell-free DNA analysis. Specifically, we propose to 1) track the dynamics of organ-specific damage, and 2) track the dynamics of T cell exhaustion during sepsis. We will do this through analysis of daily blood samples acquired from patients admitted to the intensive care unit for sepsis. Methodologically, we will achieve these through genome-wide methylation sequencing of cell-free DNA. Bioinformatically, we will then perform CIBERSORTx deconvolution to delineate and quantify specific cell/tissue types contributing to plasma cell-free DNA, thus enabling us to infer organ tissues being damaged as well as T cell exhaustion levels from both blood and tissue sources. The methods we will utilize here are highly innovative yet feasible given recent literature and our own preliminary data. Our proposed work will form the basis for a rich sepsis-focused research program utilizing cell-free DNA analysis to answer major questions in the field with the potential to ultimately improve patient survival for the deadliest disease worldwide.