Single-cell genomic profiling to identify immune signatures of bacterial sepsis in humans

单细胞基因组分析可识别人类细菌性败血症的免疫特征

• 批准号: 10210832
• 负责人: Michael Filbin
• 金额: $ 101.44万
• 依托单位: MASSACHUSETTS GENERAL HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-03-03 至 2026-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10210832
• 关键词: Accident and Emergency department; Acute; Address; Advanced Development; Affect; Antibodies; Bar Codes; Biological Markers; Biology; Blood; Blood Cells; Blood Vessels; Cell physiology; Cell surface; Cells; Cellular Indexing of Transcriptomes and Epitopes by Sequencing; Clinical; Data; Data Set; Development; Diagnostic; Diagnostic Procedure; Disease; Early Diagnosis; Endothelium; Etiology; Exhibits; Extravasation; Flow Cytometry; Functional disorder; Future; Gene Expression Profile; Gene Expression Profiling; Genes; Genomics; Goals; Health; Heterogeneity; Human; Human body; Immune; Immune System Diseases; Immune response; Individual; Infection; Intervention; Investigation; Lead; Life; Longitudinal cohort; Maps; Measures; Membrane Proteins; Modeling; Molecular; Molecular Profiling; Mus; Nature; Organ; Outcome; Pathway interactions; Patient-Focused Outcomes; Patients; Phenotype; Pilot Projects; Proteome; Rapid diagnostics; Resolution; Risk; Role; Sampling; Sepsis; Signs and Symptoms; Site; Stimulus; Surface; Symptoms; Syndrome; Technology; Testing; Therapeutic; Translating; Urinary tract infection; Validation; Variant; Vascular Endothelial Cell; Vascular Permeabilities; Work; base; biomarker panel; clinically relevant; cohort; gene function; human disease; improved; in silico; insight; monocyte; new therapeutic target; novel therapeutics; patient stratification; patient subsets; predictive marker; response; septic patients; single-cell RNA sequencing; therapeutic development; tool; transcriptome; transcriptomics

Sepsis, life-threatening organ dysfunction due to a dysregulated host response to infection, is prevalent and highly lethal. Early detection is a major challenge, largely because, as we and others showed, sepsis is a heterogeneous syndrome, with many patients presenting with vague symptoms and signs; improved biomarkers would enable earlier diagnosis, especially of these patients. A second major challenge is the shortage of treatments, as mechanisms of immune dysfunction and vascular leakage in sepsis are poorly understood, limiting therapeutic development. We hypothesize that unbiased single-cell transcriptional profiling (scRNA-seq) of circulating immune cells will identify transcriptional signatures that address both challenges. In our proof-of- principle study (Reyes et al. Nat Med 2020), we discovered a unique monocyte cell state (MS1) that is expanded in patients with urosepsis and absent in patients with milder urinary tract infection or healthy controls. MS1 discriminates septic patients from patients with other diseases in public transcriptomic data, in a second cohort of bacterial sepsis, and in preliminary data from our new cohort of patients with sepsis from any body site. Our goals in this proposal are to test the hypothesis that when extended to patients with sepsis from all body sites, unbiased single-cell approaches will generate immune signatures that distinguish sepsis from non-infectious organ dysfunction, define new clinically-relevant sepsis endotypes, identify markers that enhance sepsis diagnostics and subtyping, and reveal critical mechanistic biology underlying the immune dysfunction and vascular leak present in sepsis, thus facilitating future development of endotype-specific therapeutics. In this proposal, we will test our hypothesis that among patients presenting to the ED with acute organ dysfunction, transcriptional signatures can be identified that distinguish those with sepsis from those with non-infectious etiologies. We propose to: (1) discover blood single-cell transcriptional signatures that discriminate sepsis from non-infectious organ dysfunction, define unbiased molecular endotypes, and associate with clinical outcomes (Aim 1); (2) identify cell surface markers associated with scRNA-seq-defined cell states, including MS1, that are significantly expanded in sepsis (Aim 2); (3) define alterations in cellular functions in patients and mice with sepsis and in response to sepsis-induced MS1 cells (Aim 3). The proposed studies are highly likely to lead to substantially improved cellular and molecular signatures for sepsis that could be translated into clinical use and to new insights into the nature of immune dysregulation in sepsis. Investigations into the function of genes and pathways identified in our studies will impact mechanistic understanding of sepsis and may lead to new therapeutic concepts, especially for subsets of sepsis patients stratified based on single cell-derived molecular endotypes. Whereas sepsis remains among of the most challenging problems in human health, our use of a high-resolution unbiased approaches to address the major questions of heterogeneity and mechanism will provide highly useful datasets for the field and promote the development of new targeted therapeutics.

脓毒症是由于宿主对感染的反应失调而导致的危及生命的器官功能障碍， 非常致命早期发现是一个主要的挑战，主要是因为，正如我们和其他人所展示的那样，败血症是一种 异质性综合征，许多患者表现出模糊的症状和体征;生物标志物改善 这将有助于早期诊断，特别是对这些患者。第二个主要挑战是缺乏 治疗，因为脓毒症中免疫功能障碍和血管渗漏的机制知之甚少， 限制了治疗的发展。我们假设无偏单细胞转录谱（scRNA-seq） 循环免疫细胞将识别应对这两个挑战的转录特征。在我们的证据中- 在一项原则性研究（Reyes et al. Nat Med 2020）中，我们发现了一种独特的单核细胞状态（MS 1）， 而轻度尿路感染患者或健康对照者则不存在。MS1 在第二个队列中，在公共转录组数据中区分脓毒症患者和其他疾病患者 细菌性脓毒症，以及来自我们新的任何身体部位脓毒症患者队列的初步数据。我们 该提议的目的是检验以下假设：当扩展到全身脓毒症患者时， 无偏见的单细胞方法将产生区分败血症和非感染性的免疫特征， 器官功能障碍，定义新的临床相关的脓毒症内源性，识别增强脓毒症的标志物 诊断和分型，并揭示免疫功能障碍的关键机制生物学， 败血症中存在的血管渗漏，从而促进了未来内皮型特异性治疗剂的发展。在这 我们将检验我们的假设，即在艾德就诊的急性器官功能障碍患者中， 可以鉴定出区分脓毒症患者和非感染性脓毒症患者的转录特征， 病因学我们提出：（1）发现血液单细胞转录特征，区分败血症和 非感染性器官功能障碍，定义无偏倚的分子内型，并与临床结局相关 (Aim（2）鉴定与scRNA-seq定义的细胞状态相关的细胞表面标志物，包括MS 1，其 在脓毒症中显著扩大（目的2）;（3）定义脓毒症患者和小鼠中细胞功能的改变 脓毒症和响应脓毒症诱导的MS 1细胞（目的3）。拟议的研究极有可能导致 显著改善脓毒症的细胞和分子特征，可转化为临床应用， 对脓毒症免疫失调本质的新认识。研究基因的功能， 我们的研究中确定的途径将影响对脓毒症的机制理解，并可能导致新的 治疗概念，特别是对于基于单细胞来源的分子水平分层的脓毒症患者亚群， 内型尽管脓毒症仍然是人类健康中最具挑战性的问题之一，但我们使用 解决异质性和机制的主要问题的高分辨率无偏方法将 为该领域提供高度有用的数据集，并促进新靶向治疗的发展。