Characterising the regulatory landscape during inner ear development

表征内耳发育过程中的监管环境

• 批准号: BB/M006964/1
• 负责人: Andrea Streit
• 金额: $ 70.76万
• 依托单位: King's College London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM006964%2F1
• 关键词: Characterising; regulatory; landscape; during; inner

Hearing impairment is a debilitating condition that influences many aspects of normal life. The ability to hear is important in different contexts including for the development of speech and cognitive skills in children, for performance at work and normal social interactions in adults. Worldwide, about one of every 800 babies is born with hearing problems, while more than 50% of adults over 60 suffer from some form of hearing deficit. Hearing loss in children is often associated with defects of the inner ear, the part of the ear that houses the cells that perceive sound and balance (hair cells) and generates the neurons that transmit information to the brain. In older people, hair cells die gradually, and cannot be replaced either from other cells within the ear or through cell-based therapies. This leaves hearing aids or cochlear implants in the profoundly deaf as the only solutions.Although we have made much progress in understanding the genetic and other causes for hearing loss, there are still many conditions where the origin remains unknown. This is largely due to the complexity of the ear, but also to the fact that we still do not fully understand the dynamic genetic programme that controls ear formation in the embryo. The latter is important because mutations in many developmental genes are associated with deafness. On the other hand, many patients that present with deafness or syndromes associated with hearing impairment do not have any mutations in known genes. Here we propose to establish a complete road map for how progenitor cells, which have the potential to contribute to all sense organs, are committed to ear fate and prevented from taking up other identities. In other words, we will produce a genetic network containing the 'driving instructions' for ear formation. We have already defined distinct steps during this process, and all the players that help cells to make the correct choice at each crossroad. However, we now need to establish the sequence in which they work, how they control each other and how this process is regulated on a genome-wide level. To this end we have adapted modern molecular biology techniques to a well-studied amniote model system, the chick. The chick embryo lends itself to experimental manipulation, and importantly to rapid testing of our findings in the living embryo. We will now determine:- the genomic control regions that direct when and where each of the players is used- where and when these genomic control regions are active in inner ear cells- the 'master regulators' that interact with these genomic control regions, and hence act upstream of the players- the way in which one of the key players, the transcription factor Six1, interacts with its genomic surrounding to control the road towards ear, but away from lens fateWe will assemble this information into a large interactive network, which will be made publicly available. This network will allow us and other researchers i) to model the process of how cells become definitive ear cells by providing the detailed instructions encoded in the genome; ii) to predict the functional outcome (phenotype) caused by mutation or deletion of any of its components and vice-versa.In addition, the project will identify new candidate genes and candidate regulatory control regions for human deafness and their potential functions, provide important information for reprogramming cells into ear progenitors and for re-activating cells in the ageing ear, and provide better tools for diagnosis. Finally, because changes in genetic control regions are the critical drivers of evolutionary change and therefore for biological diversity, our data will also be exploited to study the evolution of complex sense organs.

听力障碍是一种影响正常生活许多方面的衰弱状况。听力在不同的环境中都很重要，包括儿童的言语和认知技能的发展，成年人的工作表现和正常的社会交往。在世界范围内，每800个婴儿中就有一个出生时就有听力问题，而超过50%的60岁以上的成年人患有某种形式的听力缺陷。儿童听力损失通常与内耳缺陷有关，内耳是耳朵的一部分，容纳感知声音和平衡的细胞（毛细胞），并产生将信息传递到大脑的神经元。在老年人中，毛细胞逐渐死亡，并且不能从耳内的其他细胞或通过基于细胞的治疗来替代。这使得助听器或人工耳蜗植入成为重度耳聋的唯一解决方案。尽管我们在了解遗传和其他听力损失原因方面取得了很大进展，但仍有许多情况的起源仍然未知。这在很大程度上是由于耳朵的复杂性，但也是因为我们仍然没有完全了解控制胚胎耳朵形成的动态遗传程序。后者很重要，因为许多发育基因的突变与耳聋有关。另一方面，许多患有耳聋或与听力障碍相关的综合征的患者在已知基因中没有任何突变。在这里，我们建议建立一个完整的路线图，说明具有对所有感觉器官做出贡献的潜力的祖细胞如何致力于耳朵的命运并防止其占据其他身份。换句话说，我们将产生一个包含耳朵形成“驱动指令”的遗传网络。我们已经定义了这个过程中的不同步骤，以及帮助细胞在每个十字路口做出正确选择的所有参与者。然而，我们现在需要确定它们工作的顺序，它们如何相互控制，以及这个过程如何在全基因组水平上进行调节。为此，我们采用了现代分子生物学技术，以充分研究的小鼠模型系统，小鸡。鸡胚胎适合于实验操作，重要的是，可以在活胚胎中快速测试我们的发现。我们现在将确定：-基因组控制区域，指导何时何地使用每个球员-这些基因组控制区域何时何地在内耳细胞中活跃-与这些基因组控制区域相互作用的“主调节器”，因此在球员的上游发挥作用-关键球员之一，转录因子Six 1与其基因组环境相互作用以控制通往耳朵的道路的方式，但远离透镜命运我们将把这些信息组装成一个大型互动网络，这将是公开的。这个网络将允许我们和其他研究人员i）通过提供基因组中编码的详细指令来模拟细胞如何成为最终耳细胞的过程; 2.预测功能结果（表型）的突变或缺失，反之亦然。此外，该项目将确定人类耳聋的新候选基因和候选调控区域及其潜在功能，为将细胞重编程为耳祖细胞和重新激活老化耳中的细胞提供重要信息，并为诊断提供更好的工具。最后，由于遗传控制区域的变化是进化变化的关键驱动力，因此对于生物多样性来说，我们的数据也将被用于研究复杂感觉器官的进化。

项目成果

A bioinformatics approach to building an otic gene regulatory network

构建耳基因调控网络的生物信息学方法

• 发表时间: 2016
• 作者: Anwar Maryam

Zbtb16 mediates a switch between Fgf signalling regimes in the developing hindbrain.

• DOI: 10.1242/dev.201319
• 发表时间: 2023-09-15
• 期刊: Development (Cambridge, England)

A medium-scale assay for enhancer validation in amniotes.

• DOI: 10.1002/dvdy.24306
• 发表时间: 2015-10
• 期刊: Developmental dynamics : an official publication of the American Association of Anatomists
• 作者: Chen J;Streit A
• 通讯作者: Streit A

Sox8 remodels the cranial ectoderm to generate the ear.

• DOI: 10.1073/pnas.2118938119
• 发表时间: 2022-07-12
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1

A systems-level approach reveals new gene regulatory modules in the developing ear.

• DOI: 10.1242/dev.148494
• 发表时间: 2017-04-15
• 期刊: Development (Cambridge, England)
• 作者: Chen J;Tambalo M;Barembaum M;Ranganathan R;Simões-Costa M;Bronner ME;Streit A
• 通讯作者: Streit A