Elucidating the gene regulatory networks that drive neural regeneration

阐明驱动神经再生的基因调控网络

基本信息

批准号：
10541717
负责人：
Jared A Tangeman
金额：
$ 4.07万
依托单位：
MIAMI UNIVERSITY OXFORD
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-07-01 至 2023-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10541717
关键词：
ASCL1 gene ATAC-seq Acute Address Adult Amphibia Animal Model Automobile Driving Behavior Binding Binding Sites Bioinformatics Biological Assay Cell Differentiation process Cell Nucleus Cells Characteristics Chickens Chromatin Competence Data Data Analyses Data Set Development Development Plans Embryo Environment Excision FGF2 gene Foundations Future Gene Activation Gene Expression Gene Expression Profiling Gene Expression Regulation Genes Genetic Transcription Genomics Goals Grant Homeobox Human Injury Intervention Modality Modeling Moderate Activity Multiomic Data Natural regeneration Nerve Regeneration Neural Retina Neuraxis Neurons Organism Outcome Output Phase Pigmentation physiologic function Population Positioning Attribute Postdoctoral Fellow Principal Investigator Regenerative capacity Regenerative response Regulator Genes Replacement Therapy Research Research Training Resolution Retina Role Route Small Nuclear RNA Source Structure of retinal pigment epithelium System Techniques Time Training and Infrastructure Vertebrates Work Writing Zebrafish career career development cell type computer infrastructure data handling effective therapy epigenomics experience gene regulatory network genome-wide in silico innovation insight mouse model multiple omics neurogenesis neuron regeneration novel novel strategies outreach pedagogical content programs regenerative relating to nervous system retinal damage retinal neuron skills transcription factor transcriptome sequencing transcriptomics treatment response

ASCL1 gene ATAC-seq Acute Address Adult Amphibia Animal Model Automobile Driving Behavior Binding Binding Sites Bioinformatics Biological Assay Cell Differentiation process Cell Nucleus Cells Characteristics Chickens Chromatin Competence Data Data Analyses Data Set Development Development Plans Embryo Environment Excision FGF2 gene Foundations Future Gene Activation Gene Expression Gene Expression Profiling Gene Expression Regulation Genes Genetic Transcription Genomics Goals Grant Homeobox Human Injury Intervention Modality Modeling Moderate Activity Multiomic Data Natural regeneration Nerve Regeneration Neural Retina Neuraxis Neurons Organism Outcome Output Phase Pigmentation physiologic function Population Positioning Attribute Postdoctoral Fellow Principal Investigator Regenerative capacity Regenerative response Regulator Genes Replacement Therapy Research Research Training Resolution Retina Role Route Small Nuclear RNA Source Structure of retinal pigment epithelium System Techniques Time Training and Infrastructure Vertebrates Work Writing Zebrafish career career development cell type computer infrastructure data handling effective therapy epigenomics experience gene regulatory network genome-wide in silico innovation insight mouse model multiple omics neurogenesis neuron regeneration novel novel strategies outreach pedagogical content programs regenerative relating to nervous system retinal damage retinal neuron skills transcription factor transcriptome sequencing transcriptomics treatment response

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项目摘要

Project Summary / Abstract There are no effective treatments to replace damaged retinal neurons, reflecting a fundamental inability for humans to mount robust regenerative responses within the central nervous system. To address this, it will be critical to understand the diversity of gene regulatory mechanisms that can impede or drive neuron regeneration across vertebrate contexts. Embryonic amniotes have a transitory ability to regenerate retinal neurons from cells of the retinal pigment epithelium (RPE) if supplied with exogenous FGF2 at the time of retinal injury. This mechanism of regeneration can be readily induced at embryonic day 4 (E4) of chicken development, but RPE neural competence is lost by embryonic day 5 (E5). The overarching objective of the proposed research is to profile changes in gene regulation that dispossess RPE cells of their neural competency as they differentiate. Specific aim 1 will interrogate transcription factor regulatory activity within RPE cells across the E4 / E5 developmental window by integrating gene expression analysis, chromatin accessibility profiling, and transcription factor binding assays. Preliminary bulk and single nuclei RNA-seq datasets revealed the acute activation of neural retina transcription factor profiles at both E4 and E5, such as PAX6, ASCL1, and VSX2. In contrast, genes associated with RPE maturity, such as OTX2 and pigmentation genes, were elevated in the E5 RPE independently of retinectomy and FGF2 treatment. Similarly, chromatin accessibility suggested wider dysregulation of OTX2 and related homeobox transcription factor binding sites. During the 1-year F99 phase, OTX2 binding activity will be profiled in intact and FGF2-treated RPE cells at E4 and E5 stages. Additionally, single nuclei RNA-sequencing will capture the heterogeneous transcriptional states of RPE cells during differentiation and FGF2 treatment response at E4 and E5. These results will be integrated to into a model that describes how changes in the RPE gene regulatory landscape culminates in a loss of neural competency. In specific aim 2, the gene regulatory networks present in adult vertebrate models of central nervous system regeneration will be interrogated to inspire novel routes for the induction of mammalian regeneration. This K00 phase will focus on the development of key research skills, including multi-omics data analysis approaches, techniques for spatial transcriptomics and single cell epigenomics, and cross-species genomics / transcriptomics. Up to 4 years will be spent on the K00 phase in an environment directly supportive of these applications. Specific professional development objectives will be concurrently pursued, such as pedagogical development, diversity outreach initiatives, and grant writing. Together, these aims encompass a career development plan that will lead to formation of an independent research program and result in impactful research focused on expanding human central nervous system regenerative capacity.

项目摘要 /摘要没有有效的治疗方法来替代受损的视网膜神经元，这反映了基本的无法人类在中枢神经系统内实现强大的再生反应。为了解决这个问题，它将是了解可能阻碍或驱动神经元再生的基因调节机制的多样性至关重要跨脊椎动物上下文。胚胎羊膜具有从细胞再生视网膜神经元再生的暂时性能力视网膜色素上皮（RPE）如果在视网膜损伤时为外源FGF2提供。这在鸡发育的胚胎第4天（E4）可以轻易诱导再生机制，但是RPE 胚胎第5天（E5）失去了神经能力。拟议研究的总体目标是基因调控的概况变化，使其在区分时侵犯其神经能力。特定的目标1将询问E4 / E5跨RPE细胞内的转录因子调节活性通过整合基因表达分析，染色质可及性分析和转录因子结合测定。初步散装和单核RNA-seq数据集揭示了急性 E4和E5的神经视网膜转录因子谱的激活，例如PAX6，ASCL1和VSX2。在与RPE成熟相关的基因（例如OTX2和色素沉着基因）在E5中升高 RPE独立于视网膜切除术和FGF2治疗。同样，染色质可及性建议更宽 OTX2和相关同型转录因子结合位点的失调。在1年的F99阶段， OTX2结合活性将在E4和E5阶段的完整和FGF2处理的RPE细胞中进行分析。此外，单核RNA序列将捕获RPE细胞的异质转录状态 E4和E5处的分化和FGF2治疗反应。这些结果将被整合到一个模型中描述了RPE基因调节景观的变化如何导致神经能力的丧失。在特定目标2，中枢神经系统成人脊椎动物模型中存在的基因调节网络再生将受到质疑，以激发诱导哺乳动物再生的新型途径。这个K00 阶段将重点关注关键研究技能的发展，包括多摩智数据分析方法，空间转录组学和单细胞表观基因组学的技术以及跨物种基因组学 / 转录组学。在直接支持这些环境的环境中，最多4年将花在K00阶段申请。将同时追求特定的专业发展目标，例如教学发展，多样性宣传计划和授予写作。这些目的共同涵盖了职业开发计划将导致成立独立研究计划并导致有影响力的研究专注于扩大人类中枢神经系统再生能力。