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

项目摘要 脓毒症是美国医院中最常见的死亡原因，也是死亡的头号原因。 2017年全球死亡人数达1100万人。脓毒症发病率的主要驱动因素， 死亡率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最终的 脓毒症的结果，我们有一个不完整的理解，他们的动力学和动力学。我们因此 我提出了一个双管齐下的努力，通过血浆无细胞，改变我们关于脓毒症动力学的范式 DNA法证科学化验结果具体来说，我们建议1）跟踪器官特异性损伤的动态，2）跟踪 脓毒症期间T细胞耗竭的动力学。我们将通过分析每天的血液样本 得自因败血症住进重症监护室的患者。在方法上，我们将实现 这些都是通过对游离DNA进行全基因组甲基化测序来实现的。从生物信息学的角度， 执行CIBERSORTx去卷积，以描绘和量化有助于 血浆无细胞DNA，从而使我们能够推断器官组织以及T细胞受损 从血液和组织来源的衰竭程度。我们将在这里使用的方法是高度 根据最近的文献和我们自己的初步数据，这是一种创新，但也是可行的。我们提出的工作将 形成一个丰富的脓毒症为重点的研究计划的基础，利用无细胞DNA分析， 回答该领域的主要问题，并有可能最终提高患者的生存率， 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.