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.

脓毒症是一种致命疾病，由对感染的免疫反应失调引起，影响了 700,000 人 仅在美国每年就有患者。脓毒症以及脓毒症潜在感染的早期、准确诊断是 对于治疗选择和防止严重器官损伤和死亡至关重要，但诊断选择仍然存在 有限的。该提案通过开发微创血液解决了这一未满足的医疗需求 基于循环 cfDNA 的多组学分析的测试，可同时告知宿主反应、量化器官 损伤并识别脓毒症潜在的感染 我们最近的试点工作为该提案的可行性提供了重要支持。首先，我们发现 循环游离 DNA (cfDNA) 的宏基因组测序可用于检测多种病毒和 血液中的细菌病原体。克服环境污染限制的挑战 宏基因组 cfDNA 测序的特异性我们开发了 Coffee-seq，一种宏基因组测序 对环境污染具有鲁棒性的测定。 Coffee-seq的核心思想是对DNA中的DNA进行标记 样品制备前的样品带有可通过 DNA 测序记录的标签。任何污染 标记后引入样品的 DNA 可以通过生物信息学方法进行识别和去除。我们的 原理验证工作表明，Coffee-seq 可以减少由于污染而产生的噪音 到三个数量级。 Coffee-seq 从而显着提高了宏基因组的特异性 测序分析。其次，我们开发了 cfDNA 检测方法来了解宿主组织和器官的损伤情况。这 测试采用细胞、组织和器官类型特异性的 cfDNA 甲基化标记的全基因组分析 追踪其组织来源，并量化组织特异性损伤。我们已经展示了这个的实用性 检测与尿路感染、COVID-19 和移植物抗宿主病相关的宿主组织损伤， 干细胞移植的常见并发症。 我们有两个目标：在目标 1 中，我们将测试 Coffee-seq 的实用性，以识别高脓毒症潜在的感染。 敏感性和特异性。在目标 2 中，我们将研究 cfDNA 宏基因组测序测定的效用 告知败血症相关的器官功能障碍。这是一项探索性研究，测试 cfDNA 作为多功能工具的实用性 监测脓毒症的分析物。我们将通过对 300 个生物的回顾性研究来测试这个高度转化的概念。 样本库（康奈尔大学危重疾病生物库），包括来自阳性脓毒症患者的 120 份样本 血培养，以及180份非传染性危重症患者的样本。成功实施 这项研究将为识别脓毒症潜在感染、对脓毒症亚型进行分类、监测 败血症相关的器官损伤，并指导治疗决策。