Childhood ‘Omics’ and Mycobacterium tuberculosis-derived BiOsignatures (COMBO) for TB diagnosis in high HIV prevalence settings

儿童组学和结核分枝杆菌衍生生物特征 (COMBO) 用于艾滋病毒高流行地区的结核病诊断

• 批准号: 10375468
• 负责人: Adithya Cattamanchi
• 金额: $ 51.83万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-04-22 至 2022-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10375468
• 关键词: 5 year old; Address; Africa South of the Sahara; Biological Assay; Biological Markers; Blood; Blood Banks; Cause of Death; Child; Childhood; Clinical; Communicable Diseases; Consensus; Data; Detection; Diagnosis; Diagnostic; Diagnostic tests; Disease; Enrollment; Evaluation; Failure; Gambia; Gene Expression; Gene Targeting; Genetic Transcription; HIV; HIV Infections; HIV/TB; Human; Immunity; Immunoassay; In Vitro; Investigation; Knock-out; Lead; Machine Learning; Mass Spectrum Analysis; Measurement; Measures; Methods; Microbiology; Modeling; Mus; Mycobacterium tuberculosis; Pathogenesis; Pathway Analysis; Pathway interactions; Performance; Plasma; Post-Translational Protein Processing; Prevalence; Probability; Prospective cohort; Proteins; ROC Curve; Reference Standards; Resolution; Role; Sampling; South Africa; Specificity; Sputum; Symptoms; Testing; Translating; Translations; Triage; Tryptophan; Tuberculosis; Tuberculosis diagnosis; Uganda; United States National Institutes of Health; Urine; Validation; World Health Organization; accurate diagnosis; base; bioinformatics pipeline; biomarker discovery; biomarker panel; biomarker signature; biosignature; clinical research site; clinically relevant; co-infection; cohort; cost; diagnostic accuracy; field study; in vitro Model; in vivo; in vivo Model; ion mobility; macrophage; mortality; mouse model; multiple omics; next generation; novel; pathogen; point of care; point-of-care diagnostics; prospective; protein metabolite; success; targeted biomarker; transcriptomics; tuberculosis diagnostics; validation studies

PROJECT SUMMARY There is an urgent need to develop non-sputum biomarker-based triage and diagnostic tests for childhood tuberculosis (TB). This is particularly important for young children with HIV infection, who have high TB-related mortality but often cannot produce sputum and have lower sputum bacillary burden. Biomarker discovery for childhood TB requires ultra-sensitive platforms to measure low-abundant Mycobacterium tuberculosis (Mtb) proteins in clinical samples and greater investigation of host proteins, post-translational modifications of proteins, and metabolites that are more likely than upstream RNA expression to reflect the host-pathogen interactions that lead to TB disease. The overall objective of the proposed project is to identify Mtb- and/or host-derived biosignatures in children that can achieve World Health Organization (WHO) target product profile (TPP) accuracy thresholds for a non-sputum biomarker-based triage or diagnostic test for childhood TB. We hypothesize that biosignatures that combine Mtb proteins and host biomarkers with evidence of functional relevance to TB pathogenesis or immunity will have the best diagnostic performance. To assess this hypothesis, we will conduct biomarker discovery and initial clinical validation studies using samples from three well- characterized pediatric TB cohorts in Uganda, The Gambia and South Africa. In Aim 1, we will use an ultra- sensitive electrochemoluminescence (ECL)-based immunoassay to assess the presence of Mtb proteins ESAT- 6, CFP-10, MPT64, MPT32, and Ag85B in a discovery set of banked blood and urine samples from 100 children under 5 years old with confirmed TB and 200 with unlikely TB per NIH consensus definitions (50% HIV prevalence in both groups). In Aim 2, we will use the same discovery set to perform targeted and untargeted mass spectrometry with functional assessment through pathway analysis, in vitro models and in vivo mouse models to identify host proteins, post-translational modifications and metabolites that distinguish children with confirmed versus unlikely TB. In Aim 3, we will use the candidate Mtb and host biomarkers identified in Aims 1 and 2 to derive biosignatures with up to 10 analytes consisting of Mtb proteins only, host biomarkers only, and both Mtb- and host-derived biomarkers. Biosignatures that meet WHO TPP criteria in the discovery set will 1) be evaluated in an independent test set of banked samples from 300 children under 5 years old (100 with confirmed TB, 200 with unlikely TB; 50% HIV prevalence in each group) to verify diagnostic accuracy and establish cut- offs and 2) be evaluated in a prospective cohort of 350 children under 5 years old using the pre-select cut-offs and both microbiological and clinical reference standards. Completion of these aims will result in identification of promising biosignatures that can be further validated in large-scale field studies and translated into point-of-care triage and/or diagnostic tests for childhood TB.

项目概要 迫切需要开发基于非痰生物标志物的儿童分类和诊断测试 结核病（TB）。这对于感染艾滋病毒的幼儿尤其重要，因为他们的结核病相关性很高。 死亡率较低，但通常不能产生痰且痰菌负荷较低。生物标志物发现 儿童结核病需要超灵敏平台来测量低丰度结核分枝杆菌 (Mtb) 临床样品中的蛋白质以及对宿主蛋白质、蛋白质翻译后修饰的更深入研究， 和代谢物比上游 RNA 表达更有可能反映宿主 - 病原体相互作用 导致结核病。拟议项目的总体目标是确定结核分枝杆菌和/或宿主衍生的 可以实现世界卫生组织 (WHO) 目标产品概况 (TPP) 的儿童生物特征 基于非痰生物标志物的儿童结核病分类或诊断测试的准确性阈值。我们 假设结合 Mtb 蛋白和宿主生物标志物的生物印记具有功能证据 与结核病发病机制或免疫相关的信息将具有最佳的诊断性能。为了评估这个假设， 我们将使用来自三个井的样本进行生物标志物发现和初步临床验证研究 对乌干达、冈比亚和南非的儿童结核病队列进行了特征分析。在目标 1 中，我们将使用超 基于灵敏电化学发光 (ECL) 的免疫测定法评估 Mtb 蛋白的存在 ESAT- 6、CFP-10、MPT64、MPT32 和 Ag85B，来自 100 名儿童的一组储存的血液和尿液样本 根据 NIH 共识定义，5 岁以下患有确诊结核病的儿童和 200 名不太可能患有结核病的儿童（50% HIV 两组的患病率）。在目标 2 中，我们将使用相同的发现集来执行定向和非定向 通过途径分析、体外模型和小鼠体内进行功能评估的质谱分析 识别宿主蛋白、翻译后修饰和代谢物的模型，以区分儿童 确诊结核病与不太可能结核病。在目标 3 中，我们将使用目标 1 中确定的候选 Mtb 和宿主生物标志物 2 导出最多 10 种仅由 Mtb 蛋白、宿主生物标志物组成的分析物的生物印记，以及 Mtb 和宿主衍生的生物标志物。发现集中符合 WHO TPP 标准的生物特征将 1) 对来自 300 名 5 岁以下儿童（100 名已确认的儿童）的银行样本进行独立测试集进行评估 结核病，200 不可​​能患有结核病；每组 50% 的 HIV 患病率）以验证诊断准确性并建立切入点 2) 使用预选截止值在 350 名 5 岁以下儿童的前瞻性队列中进行评估 以及微生物学和临床参考标准。完成这些目标将导致确定 有前景的生物特征，可以在大规模现场研究中进一步验证并转化为护理点 儿童结核病的分类和/或诊断测试。