Determining unique gene control mechanisms and expression patterns in children wi

确定儿童独特的基因控制机制和表达模式

• 批准号: 8881563
• 负责人: Danny Arnold Milner
• 金额: $ 49.76万
• 依托单位: HARVARD SCHOOL OF PUBLIC HEALTH
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-15 至 2015-09-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8881563
• 关键词: Affect; Africa South of the Sahara; Archives; Autopsy; Biological Markers; Biology; Blood; Blood specimen; Brain; Candidate Disease Gene; Cataloging; Catalogs; Cerebral Malaria; Cessation of life; Child; Childhood; Clinical; Clinical Data; Code; Collection; Coma; Complex; Copy Number Polymorphism; Correlation Studies; DNA; Data; Data Set; Databases; Dimensions; Disease; Frequencies; Gene Expression; Gene Family; Gene Proteins; Genes; Genetic; Genetic Polymorphism; Genetic Transcription; Genome; Genomics; Genotype; Health; Human; Hybrids; Immunohistochemistry; In Vitro; Individual; Infection; Intervention; Laboratories; Malaria; Measurement; Measures; Mediating; Molecular; Molecular Profiling; Ophthalmic examination and evaluation; Parasites; Pathogenesis; Pathway interactions; Patients; Pattern; Physiology; Plasmodium falciparum; Population; Proteins; Quantitative Trait Loci; RNA; RNA Sequence Analysis; RNA Sequences; Research Design; Retinal Diseases; Reverse Transcriptase Polymerase Chain Reaction; Risk Factors; Role; Sampling; Single Nucleotide Polymorphism; Subgroup; Syndrome; Systems Biology; Tissue Sample; Tissues; Transcript; Virulence; Virulence Factors; Virulent; base; brain tissue; case control; cohort; deep sequencing; design; digital; field study; genome sequencing; genome wide association study; human DNA; human disease; human tissue; improved; in vivo; insertion/deletion mutation; insight; meetings; mortality; nano-string; new therapeutic target; novel; peripheral blood; programs; prospective; repository; research study; tool

DESCRIPTION (provided by applicant): Interventions that thwart mortality are needed for comatose children in malaria endemic settings. These interventions require that patients who have variable disease states be carefully stratified into an exact subgroup in order to provide therapies that impact specific mortality. New interventions may come from an in depth understanding of the in vivo physiology (define by genetics and expression profiling) of the parasite which is not only unique in these children but also not reproducible in vitro. Our field study has pioneered the use of eye exams to identify malaria retinopathy in the setting of patients with clinical cerebral malaria - these findings cleanly separate patients into "true" cerebral malaria (retinopathy positive) and coma of other causes (retinopathy negative). Moreover, our database and tissue repository of over 100 pediatric autopsies from a prospective clinicopathological correlation study of cerebral malaria is the most comprehensive available. The biology of Plasmodium falciparum in vivo in cerebral malaria includes the expression of the virulent var genes as well as a set of 800 genes which are never expressed in vitro. Using an archive and prospective collection from a stringently defined cohort of comatose patients including both cerebral malaria patients and parasitemic patients with other causes of coma, we will have the opportunity to thoroughly characterize the in vivo biology of both var and unique in vivo genes of Plasmodium falciparum and understand their control and function within human disease using a comprehensive systems biology approach. We will perform full genome sequencing of parasites from patients (including clinical cases and autopsy tissues) who meet the above definitions and have low complexity infections based on our molecular genotyping tools. We will combine this full genome information with expression data from the same parasites using our novel Nanostring approach (which allows for full imputation of gene expression by measuring only 330 marker genes from minute samples of RNA) with confirmation by RNA expression and digital gene expression. The integration of these two robust data sets will allow us to define expression quantitative trait loci within the genome both directing the overall in vivo biology and specifically elucidating control and function within the unique genes found only during human infection. At the conclusion of this study, we will have defined the network of unique in vivo expressed genes during human infection, characterized the specific expression of var genes within individual patients, and identified which of these are putative targets for intervention strategies.

描述（由申请人提供）：在疟疾流行环境中，昏迷儿童需要阻止死亡的干预措施。这些干预措施要求将具有不同疾病状态的患者仔细分层为确切的亚组，以提供影响特定死亡率的治疗。新的干预措施可能来自对寄生虫体内生理学（由遗传学和表达谱定义）的深入了解，寄生虫不仅在这些儿童中是独特的，而且在体外也不可重现。我们的实地研究开创了使用眼科检查来确定临床脑型疟疾患者的疟疾视网膜病变-这些发现将患者明确分为“真正的”脑型疟疾（视网膜病变阳性）和其他原因的昏迷（视网膜病变阴性）。此外，我们的数据库和组织库中有100多例来自脑型疟疾前瞻性临床病理相关性研究的儿科尸检，是最全面的。脑型疟疾中恶性疟原虫的体内生物学包括毒性var基因的表达以及一组800个从未在体外表达的基因。使用档案和前瞻性收集从一个严格定义的昏迷患者队列，包括脑型疟疾患者和寄生虫血症患者与其他原因的昏迷，我们将有机会彻底表征体内生物学的变种和独特的体内基因的恶性疟原虫和了解他们的控制和功能，在人类疾病中使用一个全面的系统生物学方法。我们将基于我们的分子基因分型工具，对符合上述定义且具有低复杂性感染的患者（包括临床病例和尸检组织）的寄生虫进行全基因组测序。我们将联合收割机将该全基因组信息与来自相同寄生虫的表达数据结合起来，使用我们的新型Nanostring方法（该方法允许通过仅测量来自微小RNA样品的330个标记基因来完全估算基因表达），并通过RNA表达和数字基因表达进行确认。这两个强大的数据集的整合将使我们能够定义基因组内的表达数量性状基因座，既指导整体体内生物学，又具体阐明仅在人类感染期间发现的独特基因内的控制和功能。在这项研究的结论，我们将确定在人类感染过程中独特的体内表达基因的网络，表征了个体患者中var基因的特异性表达，并确定了其中哪些是干预策略的假定靶点。