Transcriptome and Network Analysis of Cleft Palate

腭裂的转录组和网络分析

基本信息

批准号：
10314049
负责人：
Ethylin Wang Jabs
金额：
$ 76.04万
依托单位：
ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-01-01 至 2024-12-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10314049
关键词：
Adhesions Affect Age Anterior Binding Biological Biomechanics CRISPR/Cas technology Cells Cleft Palate Clinical Complex Computational Biology Congenital Abnormality Critical Pathways Data Data Set Defect Development Developmental Biology Diagnosis Disease Embryo Epithelial Etiology Event FGFR2 gene Fibroblast Growth Factor Gene Expression Gene Expression Profile Gene Expression Profiling Genes Genetic Genetic Transcription Genotype Goals Growth Human Immunohistochemistry In Situ Hybridization Individual Internet Intervention Intuition Knock-in Knockout Mice Libraries Light Link Literature Maps Maxilla Medial Mediating Medical Mesenchymal Mesenchyme Methods Modeling Molecular Morphogenesis Morphology Movement Mus Mutant Strains Mice Mutation Operative Surgical Procedures Organ Culture Techniques Outcome Palate Pathologic Pathway Analysis Pathway interactions Pattern Population Prevention Process Property Psychosocial Assessment and Care RNA RNA Splicing Resolution Role SHH gene Series Signal Pathway Signal Transduction Structural Congenital Anomalies Structure System Systems Biology Technology Tissue-Specific Gene Expression Tissues Validation Wild Type Mouse Work advanced system base cell type craniofacial differential expression gene discovery human model in silico in vivo innovation insight mouse model multiple omics mutant mutant mouse model network models novel null mutation oral cleft orofacial cleft palatal shelves palatogenesis prevent psychosocial simulation single cell sequencing single-cell RNA sequencing tool transcription factor transcriptome transcriptome sequencing transcriptomics

项目摘要

ABSTRACT Cleft palate is one of the most common structural birth defects. Surgical correction and medical and psychosocial care impose significant personal and societal burdens. Increased understanding of the etiology of cleft palate potentially will lead to improvements in diagnosis and treatment. Palatogenesis is enormously complex. Paired palatal shelves first extend vertically from the maxillary processes and must grow sufficiently so that upon horizontal elevation their medial edges come into contact. Epithelia covering the medial shelves disintegrate, allowing their fusion. Key processes involved include epithelial/mesenchymal interactions and transitions. Studies in humans and mice have identified at least 429 genes associated with oral clefting. Reductionist scientific approaches have provided detail about individual genes and pathways in palatogenesis, but the intuitive models generated are not sufficient to represent the enormous complexity of the process. We will employ transcriptome and network analyses to understand how biological components work together to produce system- wide outcomes of epithelial differentiation and adhesion, mesenchymal biomechanical properties affecting remodeling and shelf elevation, and anterior/posterior regionalization of epithelia and mesenchyme. These processes require the integration of multiple cross-regulating signaling pathways. Fibroblast growth factor (FGF) and sonic hedgehog (SHH) are two such pathways, and their information is integrated with other pathways by the transcription factor p63. We will generate bulk and single-cell RNA-seq libraries from the palatal shelves of wild type mice to discover gene coexpression and regulatory networks, and specific cell populations involved in normal palatogenesis. For bulk RNA-seq libraries we will separate anterior and posterior epithelial and mesenchymal compartments allowing region-specific analysis of transcriptional changes. We will use the same approach for four mutant mouse lines, exploiting these gene perturbations to identify key driver genes and interacting pathways within these networks. We will study two activating FGFR2 mutations that exert their differential effects from the epithelium or the mesenchyme (S252W or C342Y) and null mutations of SHH and p63, expressed in the epithelium. Complementary bulk and single-cell RNA-seq libraries will identify differential gene expression and novel key components and pathways critical to palatogenesis. We will use these datasets, in conjunction with publicly available palate-related datasets to build high-resolution, multiscale molecular networks that will be used to develop predictive, mechanistic models of palatogenesis. Novel molecular networks and key regulators identified through the multiscale network modeling approach will be validated by in situ hybridization, immunohistochemistry, palatal organ cultures, and mouse models. Our innovative approach to generating comprehensive datasets, using advanced systems biology technologies, and building multiscale network models of normal and abnormal palatogenesis will have a large impact on the clinical, craniofacial, -omics, and developmental biology fields.

抽象的腭裂是最常见的结构性出生缺陷之一。手术矫正以及医疗和心理社会护理造成重大的个人和社会负担。加深对腭裂病因的了解可能会导致诊断和治疗的改进。腭发育极其复杂。配对腭架首先从上颌突垂直延伸，并且必须充分生长，以便在水平高度，它们的内侧边缘接触。覆盖内侧架的上皮分解，允许他们融合。涉及的关键过程包括上皮/间质相互作用和转变。对人类和小鼠的研究已鉴定出至少 429 个与口裂相关的基因。还原论者科学方法提供了有关腭发育中个体基因和途径的详细信息，但直观的方法生成的模型不足以代表该过程的巨大复杂性。我们将聘用转录组和网络分析，以了解生物成分如何协同工作以产生系统- 上皮分化和粘附的广泛结果，间充质生物力学特性影响重塑和架抬高，以及上皮和间质的前/后区域化。这些过程需要整合多个交叉调节信号通路。成纤维细胞生长因子（FGF）和声波刺猬（SHH）是这样的两个通路，它们的信息通过以下方式与其他通路整合：转录因子p63。我们将从腭架中生成批量和单细胞 RNA-seq 文库野生型小鼠发现基因共表达和调控网络，以及参与其中的特定细胞群正常的腭发育。对于批量 RNA-seq 文库，我们将分离前上皮和后上皮，间充质区室允许对转录变化进行区域特异性分析。我们将使用相同的四种突变小鼠品系的方法，利用这些基因扰动来识别关键驱动基因和这些网络内的相互作用路径。我们将研究两种激活 FGFR2 的突变，它们发挥其作用来自上皮或间质（S252W 或 C342Y）的差异效应以及 SHH 和的无效突变 p63，在上皮细胞中表达。互补的批量和单细胞 RNA-seq 文库将识别差异对腭发育至关重要的基因表达以及新的关键成分和途径。我们将使用这些数据集，结合公开可用的味觉相关数据集来构建高分辨率、多尺度分子将用于开发腭发育的预测性机械模型的网络。新颖的分子网络通过多尺度网络建模方法确定的关键监管机构将通过现场验证杂交、免疫组织化学、腭器官培养和小鼠模型。我们的创新方法使用先进的系统生物学技术生成综合数据集，并构建多尺度正常和异常腭发育的网络模型将对临床、颅面、 -组学和发育生物学领域。