Developmental reprogramming and transorganogenesis

发育重编程和跨器官发生

基本信息

批准号：
10588050
负责人：
Joel H. Rothman
金额：
$ 33.43万
依托单位：
UNIVERSITY OF CALIFORNIA SANTA BARBARA
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-04-01 至 2028-02-28
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10588050
关键词：
ATAC-seq Adult Animals Architecture Autophagocytosis Auxins Binding Biological Caenorhabditis elegans Cell Cycle Cell Cycle Inhibition Cell Differentiation process Cell Nucleus Cells Characteristics Chromatin Code Congenital Abnormality Data Pooling Development Elasticity Embryo Endoderm Endowment Event Extinction Gastrointestinal tract structure Gene Expression Gene Expression Profile Generations Genes Genetic Genetic Transcription Genomics Germ Cells Goals Gonadal structure Hand Heat-Shock Response Human Maintenance Malignant Neoplasms Mediating Metaplasia Methods Molecular Morphology Mutation Nature Nuclear Organ Pathway interactions Pattern Pharyngeal structure Predisposition Process Program Development Property Proteins Recovery Refractory Regenerative Medicine Research Resistance Role Specific qualifier value Statistical Data Interpretation Stereotyping System Testing Untranslated RNA Up-Regulation Uterus Variant attenuation causal variant cell type developmental plasticity genetic selection genome-wide human stem cells in vivo insight malformation member multiple omics mutant pathogen postmitotic premalignant prevent progenitor protein degradation replacement tissue response transcription factor transcriptome transdifferentiation whole genome

项目摘要

SUMMARY The major objectives of the proposed research are to illuminate the cellular and molecular mechanisms that control developmental plasticity and to investigate how post-mitotic differentiated cells in an intact animal can be reprogrammed and remodeled into new cell types in the process of transdifferentiation (Td). The well-described pathway for endoderm development in C. elegans will be applied to molecularly dissecting Td and “transorganogenesis” (conversion of one organ into another). One component in this pathway, the C. elegans ELT-7 GATA transcription factor, is capable of converting differentiated, post-mitotic cells of two organs, the pharynx and uterus, into cells with gene expression patterns and ultrastructural characteristics of normal gut cells. Highly dynamic changes in the transcriptome occur during this remarkable process, and six stages (promiscuity, attenuation, extinction, rebound, persistence, and remodeling) can be resolved during Td based on gene expression and altered cellular and organ morphology. These events define Td-competent (Td+) cells that convert to gut-like cells and Td-resistant (Td-) cells that only transiently permit ELT-7 to activate its target. Among the genes whose expression undergoes upregulation during Td are sets of genes associated with protein turnover, autophagy, and the intracellular pathogen response (IPR), suggesting that these pathways play a role in Td. On the basis of ELT-7-induced developmental arrest, two genetic selections were developed that identify large numbers of mutants defective in Td. With these preliminary findings in hand, we will probe the mechanisms of Td through three Specific Aims. In SA1, we will investigate the dynamics of cellular remodeling, test the hypothesis that turnover processes of protein degradation and autophagy participate in key stages of Td and remodeling, assess the role of the IPR in Td, and investigate the action of cell-cycle exit in the Td process. In SA2, we will evaluate whether differences between single Td+ and Td- cells of varied differentiated cell types can be ascribed to their unique transcriptome dynamics and will test the hypothesis that changes in chromatin architecture of Td- cells, assessed by ATAC-seq, initially and transiently proceed through similar patterns to those of Td+ cells, with elastic reversion to the original state. In SA3, we will characterize mutants from two genetic selections that are defective in ELT-7-mediated developmental arrest and Td and will use them to investigate interdependence of the six stages of Td. We will identify the causal gene(s) underlying large numbers of mutants defective in Td by a high-throughput method based on statistical analysis of variants in pooled genome-wide sequences, including those coding for proteins and non-coding RNAs. These studies may advance our understanding of mechanisms involved in pre-cancerous metaplasias of the digestive tract. They will also provide insights into the mechanisms of organ malformation in birth defects and could lead to methods for reprogramming differentiation for organ generation in regenerative medicine.

概括拟议研究的主要目标是阐明细胞和分子机制控制发育可塑性，并研究如何在完整动物中的有丝分化后分化细胞在转变过程（TD）的过程中重新编程并重塑为新的细胞类型。描述的秀丽隐杆线虫中内胚层发育的途径将应用于分子解剖TD和 “跨组织发生”（一个器官转化为另一个器官）。秀丽隐杆线虫中的一个组成部分 ELT-7 GATA转录因子，能够转化两个器官的分化后的有丝分裂细胞，咽部和子宫进入具有基因表达模式和正常肠道超微结构特征的细胞细胞。在这个非凡的过程中，转录组的高度动态变化发生，六个阶段发生（滥交，衰减，扩展，反弹，持久性和重塑）可以在基于TD的过程中解决关于基因表达以及细胞和器官形态的改变。这些事件定义了TD竞争力（TD+）细胞转换为肠状细胞和抗TD抗性细胞（TD-）细胞，这些细胞仅暂时允许ELT-7激活其靶标。在TD期间表达上调的基因中，与蛋白质相关的基因集营业额，自噬和细胞内病原体反应（IPR），表明这些途径起着作用在TD中。根据ELT-7诱导的发育停滞，开发了两种遗传选择，以识别大量突变体在TD中有缺陷。有了这些初步发现，我们将探测机制通过三个特定目标的TD。在SA1中，我们将研究细胞重塑的动力学，测试假设蛋白质降解和自噬参与TD的关键阶段和自噬的过程重塑，评估IPR在TD中的作用，并研究细胞周期退出在TD过程中的作用。 SA2，我们将评估各种分化细胞类型的单个TD+和TD细胞之间的差异是否可以归因于其独特的转录组动力学，并将测试染色质变化的假设最初，瞬时地通过与 TD+细胞的那些，弹性反向原始状态。在SA3中，我们将表征来自两个的突变体在ELT-7介导的发育停滞和TD中有缺陷的遗传选择，并将使用它们来研究TD的六个阶段的相互依赖性。我们将确定大量的因果基因基于汇总变体的统计分析，通过高通量方法在TD中有缺陷的突变体全基因组序列，包括编码蛋白质和非编码RNA的序列。这些研究可能会进步我们对消化道前癌前代理的机制的理解。他们也会提供有关先天缺陷中器官畸形机制的见解，并可能导致方法重新编程为再生医学中器官产生的分化。