Patient Sampling and Genomics Core

患者采样和基因组学核心

• 批准号: 10491060
• 负责人: STEVEN M DUDEK
• 金额: $ 36.25万
• 依托单位: UNIVERSITY OF ILLINOIS AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-20 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10491060
• 关键词: Acute; Acute Lung Injury; Acute Respiratory Distress Syndrome; African American; Bioinformatics; Biometry; Blood; Blood specimen; Bronchoalveolar Lavage; Clinical; Clinical Data; Code; Critical Illness; Data; Development; Diagnostic; Disease Outcome; Doctor of Philosophy; Enrollment; Etiology; Excision; Genomics; Hispanic; Human; Human Resources; Immune Tolerance; Individual; Inflammatory; Informatics; Institutional Review Boards; Latino; Lung; Lymphocyte; Mechanical ventilation; Mediating; Medicine; Methodology; Pathway interactions; Patients; Peripheral Blood Mononuclear Cell; Pharmacology; Phase; Phenotype; Pneumonia; Population; Process; Protocols documentation; Pulmonology; Reporting; Research; Research Personnel; Resolution; Resources; Role; Safety; Sampling; Sepsis; Severities; Severity of illness; Specialist; Specimen; Structure; Underrepresented Populations; Universities; Work; biobank; clinical database; clinical phenotype; improved; innovation; lung injury; macrophage; novel strategies; patient population; patient subsets; professor; programs; repaired; repository; respiratory; sample collection; sepsis induced ARDS; single-cell RNA sequencing; transcriptome sequencing; transcriptomics; treatment response

PROJECT SUMMARY / ABSTRACT A critical translational component of this Program Project involves the correlative analysis of macrophages (Mφ) isolated from critically ill patients suffering from sepsis, pneumonia, and other acute insults that result in the devastating clinical syndrome of Acute Respiratory Distress Syndrome (ARDS). The Patient Sampling and Genomics Core (Core D) will perform the central function of collecting these Mφ samples and establishing and maintaining a clinical database of disease severity. Feasibility for obtaining sufficient samples for the proposed studies will be greatly enhanced through extensive utilization of a non-bronchoscopic BAL (NBBAL) approach, which results in diagnostic yields similar to bronchoscopic BAL and has an excellent safety profile in critically ill patients requiring mechanical ventilation. In addition, blood will be collected for isolation of peripheral blood mononuclear cells (PBMCs) for comparison with lung samples. Longitudinal samples will be collected from a subset of patients. Additionally, Core D will provide biostatistical analysis on these clinical samples as well as bioinformatic analysis on samples from all Projects, including bulk RNA-seq analysis, and single-cell RNA-seq (scRNA-seq) processing and analysis, as described in the individual Projects. A spectrum of clinical severity will be obtained to correlate disease outcomes with flow cytometric, transcriptomic, and functional analyses of Mφs, focusing on pathways relevant to each of the four Projects. Innovative aspects of this Core include the following: a) development of an unique biorepository of lung Mφ samples from patients with ARDS, including longitudinal samples from a subset of patients to characterize changes in lung Mφ populations during the phases of ARDS; b) scRNA-seq analysis of patient lung Mφ, representing a substantial methodological advance in Mφ analysis compared to other recent studies; c) extensive utilization of the NBBAL approach to greatly enhance sample collection since it can be performed safely and with high yield by respiratory therapists and fellow trainees; d) an integrated Core structure that combines patient sample acquisition with biostatistical and bioinformatic expertise and resources to maximize efficient utilization of these clinical data; e) sample collection from a diverse ICU patient population of under-represented and insufficiently studied groups (30-40% African-American and 30-40% Hispanic/Latino patients). f) Comparison of expression profiles in lung Mφ populations from ARDS patients with circulating PBMCs after removal of lymphocytes, which will improve the reported poor correlation between these sample types; g) inclusion of immune paralysis as phenotypic characterization of patient samples, which has not been evaluated in past studies of ARDS AMφ clinical samples; h) enhanced focus on sepsis and pneumonia-induced ARDS as the primary etiologies characterized by intensive lung Mφ analysis.

项目总结/摘要 该项目的一个关键翻译部分涉及巨噬细胞（Mφ）的相关性分析 从患有败血症、肺炎和其他急性损伤的重症患者中分离， 急性呼吸窘迫综合征（ARDS）的毁灭性临床综合征。患者采样和 基因组学核心（核心D）将执行收集这些Mφ样本并建立 维护疾病严重程度的临床数据库。获得足够样本的可行性 通过广泛使用非支气管镜BAL（NBBAL）方法将大大增强研究， 其诊断率与支气管镜BAL相似，并且在危重患者中具有极佳的安全性 需要机械通气的患者。此外，还将采集血液用于外周血分离 单核细胞（PBMC）用于与肺样品比较。纵向样本将从一个 患者的子集。此外，核心D将提供这些临床样本的生物统计学分析，以及 对所有项目的样品进行生物信息学分析，包括批量RNA-seq分析和单细胞RNA-seq分析 （scRNA-seq）处理和分析，如各个项目中所述。一系列临床严重程度将 获得与Mφ的流式细胞术、转录组学和功能分析相关的疾病结果， 重点是与四个项目中的每一个项目相关的途径。 该核心的创新方面包括：a）开发一种独特的肺生物储存库， 来自ARDS患者的Mφ样本，包括来自患者子集的纵向样本，以表征 在ARDS阶段期间肺Mφ群体的变化; B）患者肺Mφ的scRNA-seq分析， 与其他最近的研究相比，代表Mφ分析的实质性方法学进步; c）广泛 利用NBBAL方法大大提高样本采集，因为它可以安全地进行， 呼吸治疗师和学员学员的高产量; d）一个综合的核心结构， 利用生物统计学和生物信息学专业知识和资源进行样本采集，以最大限度地提高利用率 e）从代表性不足的不同ICU患者人群中采集样本， 研究不充分的人群（30-40%的非洲裔美国人和30-40%的西班牙裔/拉丁裔患者）。f）比较 在去除肺内巨噬细胞后，来自ARDS患者的肺Mφ群体与循环PBMC的表达谱 淋巴细胞，这将改善这些样品类型之间报告的不良相关性; 免疫麻痹作为患者样本的表型表征，过去未对其进行评价 h）加强对脓毒症和肺炎诱导的ARDS的关注， 以肺Mφ分析为特征的主要病因。