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3D imaging and deep sequencing of gene expression in the genital tubercle

生殖结节基因表达的 3D 成像和深度测序

基本信息

批准号：
8926970
负责人：
MARTIN J COHN
金额：
$ 29.45万
依托单位：
UNIVERSITY OF FLORIDA
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-09-30 至 2016-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8926970
关键词：
Affect Arts Atlases Cell Therapy Cells Child Cloaca Chamber Colon Colorectal Communities Congenital Abnormality Data Detection Development Developmental Anatomy Distal Endocrine Disruptors Endoderm Endoderm Cell Epithelial Cells Epithelium Exposure to Failure Foundations Future Gene Expression Gene Expression Profile Generations Genes Genetic Genetic Programming Genetic Screening Genetic study Genital system Genitalia Genitourinary system Goals Human Hypospadias Image Incidence Knowledge Limb Bud Limb Development Link Live Birth Maps Mesenchyme Modeling Molecular Molecular Profiling Morphogenesis Natural regeneration Noise Operative Surgical Procedures Optics Outcome Pattern Perinatal Exposure Play Population Protein Isoforms Public Health RNA Sequences RNA Splicing Reagent Relative (related person)Research Role Staging Stem cells Technology Three-Dimensional Imaging Tissues Transcript Tube Urethra Urothelium Variant ambiguous genitalia base cell type deep sequencing digital external genitalia gene discovery gene function innovation malformation molecular marker mouse model novel novel marker penis penis foreskin prepuce progenitor repaired research study tomography tool transcriptome sequencing urologic

项目摘要

DESCRIPTION (provided by applicant): The most common anomaly of the genitourinary system is hypospadias, a malformation of the external genitalia that is characterized by failure of urethral tube closure and incomplete formation of the prepuce (foreskin) and ventral penis. The incidence of hypospadias has more than doubled over the past 30 years, without explanation, and it is now the second most common birth defect in humans, affecting an estimated 1 of every 250 live births. Whether the causes of hypospadias are genetic, environmental, or a combination of both, development of preventative strategies for hypospadias and of cell-based therapies for repair of urologic tissues will require knowledge of the genetic programs that direct cell fate decisions and tissue morphogenesis. Identification of these mechanisms first requires the establishment of a foundation of descriptive data, in the form of gene expression patterns, for the different tissue compartments of the lower genitourinary tract. Moreover, transcriptional profiling will need to be linked to developmental anatomy in order to formulate hypotheses regarding gene function during morphogenesis, and to consider how multiple genes may interact within a tissue or cell population. In preliminary studies using microarrays, we identifie 86 novel markers of the urethral epithelium of the El 2.5 genital tubercle. Here we propose to use OPT to build a 3D reference model of the genital tubercle, and to map the expression domains of each of these genes onto the reference tubercle to create a 3D, multi-gene atlas of the gene expression in the developing external genitalia. We will build upon these results in two ways. Firstly, we will extend the OPT atlas to two additional stages of external genital development. Secondly, we will drill deeper into the expression profiling by using NexGen sequencing technology (RNA-seq) to characterize the quantitative patterns of gene expression and the distribution of splice variants in the endodermal cells fated to form the urethral epithelium. This combination of approaches will provide a wealth of new cell type-specific markers, uncover the quantitative molecular profiles of urethral progenitors, and place these data in a 3D developmental anatomical context that can be utilized by the research community for future hypothesis-based studies.

描述(申请人提供)：最常见的泌尿生殖系统异常是尿道下裂，这是一种外生殖器畸形，其特征是尿管闭合，包皮(包皮)和腹侧阴茎形成不全。在过去的30年里，尿路下裂的发病率增加了一倍多，原因不明，它现在是人类第二常见的出生缺陷，估计每250名活产中就有一名受到影响。无论尿道下裂的原因是遗传的、环境的，还是两者的组合，开发用于尿路下裂的预防策略和基于细胞的尿路组织修复疗法都需要了解指导尿路下裂的遗传程序细胞命运决定和组织形态发生。要确定这些机制，首先需要以基因表达模式的形式为下生殖道的不同组织间隔建立描述性数据基础。此外，转录图谱将需要与发育解剖学联系起来，以便制定关于形态发生过程中基因功能的假设，并考虑多个基因如何在组织或细胞群体中相互作用。在利用微阵列进行的初步研究中，我们确定了EL 2.5生殖器结节的尿路上皮的86个新标记。在这里，我们建议使用OPT来构建生殖器结节的3D参考模型，并将每个基因的表达结构域映射到参考结节上，以创建发育中的外生殖器中基因表达的3D、多基因图谱。我们将在这些成果的基础上采取两种方式。首先，我们将把OPT图谱扩展到外生殖器发育的另外两个阶段。其次，我们将利用NexGen测序技术(RNA-seq)更深入地研究表达谱，以表征基因表达的定量模式和剪接变体在注定要形成尿路上皮的内皮细胞中的分布。这种方法的结合将提供丰富的新的细胞类型特异性标记，揭示尿道祖细胞的定量分子图谱，并将这些数据置于3D发育解剖学环境中，研究界可以利用这些数据进行未来基于假设的研究。