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.

项目摘要 迫切需要开发基于生物标志物的非估计分类和童年的诊断测试 结核病（TB）。这对于艾滋病毒感染的幼儿尤其重要，与TB有关 死亡率，但通常无法产生痰液，并且具有较低的痰液杆菌负担。生物标志物发现 儿童结核病需要超敏感的平台来测量低多余的分枝杆菌结核病（MTB） 临床样品中的蛋白质和对宿主蛋白的更多研究，蛋白质的翻译后修饰， 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 导致结核病疾病。拟议项目的总体目标是确定MTB-和/或主机衍生的 可以实现世界卫生组织（WHO）目标产品概况（TPP）的儿童的生物签名 基于非估计生物标记物的分类或儿童结核病诊断测试的精度阈值。我们 假设将MTB蛋白和宿主生物标志物与功能性的证据相结合的生物签名 与结核病发病机理或免疫力相关的性能将具有最佳的诊断性能。为了评估这一假设， 我们将使用来自三个井的样品进行生物标志物发现和初始临床验证研究 在乌干达，冈比亚和南非的小儿结核病队列的特征。在AIM 1中，我们将使用超级 敏感电化学发光（ECL）的免疫测定法评估MTB蛋白ESAT-的存在 6，CFP-10，MPT64，MPT32和AG85B在发现100个儿童的一组存放血液和尿液样本中 5岁以下的结核病确认和200岁，每NIH共识定义不太可能（50％艾滋病毒） 两组的患病率）。在AIM 2中，我们将使用相同的发现集来执行针对性和不靶向 通过途径分析，体外模型和体内小鼠进行功能评估的质谱法。 识别宿主蛋白质，翻译后修饰和代谢产物的模型，以区分儿童 确认与不太可能的结核病。在AIM 3中，我们将使用AIMS 1中确定的候选MTB和主机生物标志物 和2个以多达10种由MTB蛋白组成的分析物来得出生物签名，仅宿主生物标志物，并且 MTB和宿主衍生的生物标志物。在发现集中符合谁TPP标准的生物签名将为1） 在来自5岁以下的300名儿童的独立测试集中评估（确认有100名儿童） TB，200个不太可能的结核病；每组的HIV患病率为50％），以验证诊断准确性并建立临界值 OFF和2）使用预选前的截止者在350名550岁以下的350名儿童中进行评估 以及微生物和临床参考标准。这些目标的完成将导致确定 可以在大规模现场研究中进一步验证的有希望的生物签名并转化为护理 儿童结核病的分类和/或诊断测试。