Cell-free DNA as a versatile analyte for the monitoring of sepsis

游离 DNA 作为监测脓毒症的多功能分析物

• 批准号: 10665402
• 负责人: Iwijn De Vlaminck
• 金额: $ 24.42万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-02-06 至 2025-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10665402
• 关键词: Acute Renal Failure with Renal Papillary Necrosis; Address; Affect; Bioinformatics; Biological Assay; Blood; Blood Tests; COVID-19; Cell Death; Cells; Cessation of life; Chemistry; Classification; Clinical; Coffee; Complication; Critical Illness; Cytosine; DNA; DNA sequencing; Data; Data Set; Deamination; Development; Diagnostic; Early Diagnosis; Environmental Pollution; Enzymes; Functional disorder; Genome; Goals; Health Care Costs; Hospitalization; Immune response; Incidence; Infection; Injury; Injury to Kidney; Kidney Diseases; Label; Measurement; Medical; Metagenomics; Methylation; Modeling; Monitor; Morbidity - disease rate; Noise; Non-Invasive Detection; Oligonucleotides; Organ; Organ failure; Outcome; Patients; Performance; Persons; Preparation; Retrospective Studies; Sampling; Sensitivity and Specificity; Sepsis; Sodium Chloride; Specificity; Stem cell transplant; Testing; Tissues; Urinary tract infection; Work; accurate diagnosis; biobank; bisulfite; cell free DNA; cell type; cohort; end stage liver disease; experimental study; genome-wide; graft vs host disease; improved; innovation; liver injury; metagenomic sequencing; microorganism; minimally invasive; mortality; multiple omics; next generation sequencing; organ injury; pathogenic bacteria; pathogenic virus; prevent; septic patients; tissue injury; treatment choice

Sepsis is a deadly condition caused by a dysregulated immune response to infection which affects 700,000 patients per year in the US alone. Early and accurate diagnosis of sepsis, and infection underlying sepsis is critical to inform treatment choices and to prevent serious organ injury and death, but diagnostic options remain limited. This proposal addresses this unmet medical need with the development of a minimally invasive blood test based on a multi-omics profiling of circulating cfDNA to simultaneously inform host responses, quantify organ injury and identify infection underlying sepsis Our recent pilot work provides significant support for the feasibility of this proposal. First, we have found that metagenomic sequencing of circulating cell-free DNA (cfDNA) can be used to detect a broad range of viral and bacterial pathogens in blood. To overcome the challenge of environmental contamination which limits the specificity of metagenomic cfDNA sequencing we have developed Coffee-seq, a metagenomic sequencing assay that is robust against environmental contamination. The core idea of Coffee-seq is to tag the DNA in the sample prior to sample preparation with a label that can be recorded by DNA sequencing. Any contaminating DNA that is introduced in the sample after tagging can then be bioinformatically identified and removed. Our proof-of-principle work demonstrates that Coffee-seq leads to a reduction of noise due to contamination by up to three orders of magnitude. Coffee-seq thereby dramatically improves the specificity of metagenomic sequencing assays. Second, we have developed cfDNA assays to inform injury to host tissues and organs. This test employs genome-wide profiling of methylation marks of cfDNA that are cell, tissue and organ-type specific to trace their tissues-of-origin, and to quantify tissue-specific injury. We have demonstrated the utility of this assay to identify host-tissue injury related to urinary tract infection, COVID-19, and Graft-Versus Host Disease, a frequent complication of stem cell transplantation. We have two aims: In Aim 1, we will test the utility of Coffee-seq to identify infection underlying sepsis with high sensitivity and specificity. In Aim 2, we will investigate the utility of a cfDNA metagenomic sequencing assay to inform sepsis related organ dysfunction. This is an exploratory study that tests the utility of cfDNA as a versatile analyte to monitor sepsis. We will test this highly translational concept with a retrospective study of 300 bio- banked samples (Cornell Biobank of Critical Illness), including 120 samples from septic patients with positive blood culture, and 180 samples from patients with non-infectious critical illness. Successful implementation of this study will lead to new avenues to identify infection underlying sepsis, to classify sepsis subtypes, to monitor sepsis-related organ damage, and to guide treatment decisions.

败血症是由于对感染的免疫反应失调引起的致命状况，影响700,000 仅在美国，每年的患者。败血症的早期，准确诊断，败血症的感染是 为治疗选择提供信息至关重要，防止严重的器官损伤和死亡，但诊断选择仍然 有限的。该提案通过开发微创血液来解决这种未满足的医疗需求 基于循环cfDNA的多词分析的测试，以同时告知宿主响应，量化器官 受伤并识别败血症的感染 我们最近的试点工作为该提案的可行性提供了重大支持。首先，我们发现 循环无细胞DNA（CFDNA）的元基因组测序可用于检测广泛的病毒范围和 血液中的细菌病原体。克服环境污染的挑战，这限制了 元基因组CFDNA测序的特异性我们开发了咖啡赛，一种元基因组测序 对环境污染的强大测定。咖啡播种的核心思想是标记DNA 样品在样品制备之前使用可以通过DNA测序记录的标签。任何污染 然后可以在标记后引入样品中引入的DNA，然后将生物信息鉴定并去除。我们的 原理证明的工作表明，咖啡播种会导致由于上UP的污染而降低噪音 到三个数量级。因此，咖啡秘密大大提高了元基因组的特异性 测序测定法。其次，我们开发了CFDNA分析，以告知宿主组织和器官的伤害。这 测试采用细胞，组织和器官特异性的CFDNA甲基化标记的全基因组分析 追踪其原始组织，并量化组织特异性损伤。我们已经证明了这一点的实用性 测定与泌尿道感染有关的宿主组织损伤，COVID-19和移植物与宿主疾病， 经常发生干细胞移植的并发症。 我们有两个目标：在AIM 1中，我们将测试咖啡塞克的效用，以鉴定高败血症的感染 灵敏度和特异性。在AIM 2中，我们将研究CFDNA元基因组测序测定的实用性 告知相关的器官功能障碍。这是一项探索性研究，可以测试CFDNA作为多功能的实用性 分析物监测败血症。我们将通过对300个生物的回顾性研究来测试这种高度转化的概念 银行样品（康奈尔生物库的危重疾病），包括来自阳性化粪池患者的120个样本 血液培养和来自非感染性重症患者的180个样本。成功实施 这项研究将导致新的途径鉴定败血症的感染，以对败血症进行分类，以监测 败血症相关的器官损伤，并指导治疗决策。