Functional Genomic Study of Aging and Aging Interventions

衰老是一个生物学过程，其特征是各种生理功能逐渐衰退。有许多与年龄相关的变化，包括基因表达的变化，从酵母、蠕虫、苍蝇、啮齿动物、非人类灵长类动物和人类等各种生物中都有。老龄化领域的一个重要问题是，这些与年龄相关的变化是否以及如何调节健康寿命和寿命。 包括线虫和黑腹线虫在内的无脊椎动物模型处于研究的前沿，以确定衰老过程的分子机制。利用无脊椎动物进行衰老研究的优势不仅包括它们的寿命相对较短，通常不到几个月，便于跟踪它们的一生，而且还可以获得丰富的遗传和基因组资源，用于强大的遗传和分子研究。我们在2013年发表的一篇综述论文中总结了无脊椎动物模型在老龄化研究中的重要性。我们还在2013年发表在《分子生物学方法》上的一篇综述论文中详细介绍了果蝇的衰老方案。这些出版物应该为无脊椎动物，特别是线虫和黑腹线虫的衰老研究提供有价值的指导。 像许多其他生物一样，在两个强大的无脊椎动物模型--秀丽线虫和黑腹线虫中，衰老与数千个基因的表达变化有关。与这些分子变化相关的一个中心问题是，它们是否提供了与人类衰老相关的任何分子洞察力。解决这个问题的一种方法是确定线虫和黑腹线虫之间哪些分子变化在进化上是保守的。这些保守的变化可能有助于理解适用于人类衰老的分子机制。然而，尽管有许多生物信息学方法可用于识别保守的基因和蛋白质，但工具有限，无法识别序列相似性低但功能保守的基因和蛋白质，后者可能由基因组的很大一部分组成。为了解决这个问题，我们与Kevin Becker博士和Ilya Goldberg博士领导的几个内部小组合作，开发了一个生物信息学工具，用于高通量分析线虫和黑腹线虫之间的大量基因集。我们已经证明了这些基因组在包括衰老在内的复杂生物表型的系统生物学研究中的实用性。这项工作已发表在《BMC基因组学2013》上。本文描述的工具和数据库将使我们能够更好地利用包括人类在内的许多生物中可用的大量基因组数据，并有助于在未来的研究中研究各种生物过程中的功能保守，如衰老。 在与衰老过程相关的保守蛋白质中，拓扑异构酶是已知的解决DNA拓扑蛋白所必需的，并且对衰老相关的生物过程，如DNA修复至关重要。RNA代谢已被证明在几乎所有的生物过程中都是至关重要的，包括衰老和许多疾病，如与年龄相关的退行性疾病。然而，没有一种真核拓扑异构酶与RNA代谢相关。在与王卫东博士的合作中，我们确定top3&946；是第一个真核RNA拓扑异构酶，它存在于细胞中的多聚核糖体和应激颗粒中。我们进一步证明了top3&946；与脆性X蛋白(FMRP)相互作用调节果蝇神经肌肉接头(NMJ)的突触形成。FMRP是一种与脆性X综合征和自闭症有关的主要蛋白质。脆性X综合征是一种常见的智力残疾形式。我们已经证明，Top3和FMRP结合了许多常见的mRNAs，包括那些由与精神分裂症和自闭症相关的神经功能基因编码的mRNAs。Top3&946；基因突变已被证明与人类的精神分裂症和智力残疾有关。这些发现表明，top3&946；在RNA新陈代谢中扮演着RNA拓扑异构酶的角色，并与FMRP相互作用，促进神经发育和心理健康。这项工作发表在《自然神经科学》(2013)上。第一个真核RNA拓扑异构酶的发现将有助于确定RNA代谢，特别是拓扑结构在衰老和神经系统疾病中的作用，这将为衰老领域的研究开辟一条新的道路。 综上所述，我们在了解衰老和年龄相关疾病的分子机制方面取得了重大进展。我们已经开发了一种用于高通量基因组数据功能研究的生物信息学工具。我们已经鉴定了第一个RNA拓扑异构酶，并证明了它在维持心理健康方面的作用。这些研究对于促进翻译老年学分会的目标和NIA了解衰老的基本生物学和开发有效的人类干预措施的使命是有价值的。

Aging is a biological process that can be characterized as a gradual decline of various physiological functions. There are numerous age-related changes, including changes in gene expression, that are shared in various organisms ranging from yeast, worm, fly, rodent, non-human primates and humans. One of the important questions in the aging field is whether and how these age-related changes modulate healthspan and lifespan. Invertebrate models, including C. elegans and D. melanogaster, are in the forefront of studies to determine the molecular mechanisms underlying aging processes. The advantages of using invertebrates for aging studies include not only their relative short lifespan, typically in shorter than a few months for the ease to follow their whole life, but also the availability of rich genetic and genomic resource for powerful genetic and molecular studies. We have summarized the important of invertebrate models in aging research in a review paper published Ageing Research Reviews (2013). We have also detailed aging protocols in Drosophila in a review paper published in Methods in Molecular Biology 2013. These publications should provide valuable guidance for aging research in invertebrates, especially C. elegans and D. melanogaster. Like many other organisms, aging is associated with expression changes of thousands of genes in two powerful invertebrate models, C. elegans and D. melanogaster. A central question related to these molecular changes is whether they provide any molecular insight relevant to human aging. One approach to address this issue is to identify which molecular changes are evolutionarily conserved between C. elegans and D. melanogaster. The conserved changes will likely help understand molecular mechanisms applicable to human aging. However, despite of many bioinformatic approaches available to identify conserved genes and proteins mostly based on sequence homolog, tools are limited to identify genes and proteins with low sequence similarity but conserved function, the latter of which likely consist of a significant portion of genome. To address this issue, in collaboration with several intramural groups directed by Drs. Kevin Becker and Ilya Goldberg, we have developed a bioinformatic tool for high throughput functional analysis of large number of gene sets between C. elegans and D. melanogaster. We have demonstrated the utility of these gene sets in systems biology studies of complex biological phenotypes, including aging. This line of work has been published in BMC Genomics 2013. The tool and database described in this paper will allow us taking better advantage of large amount of genomic data available in many organisms including humans and facilitate the studies of functional conservation in various biological processes, such as aging, in the future studies. Among the conserved proteins related to aging processes are topoisomerases, which are known to be essential to solve DNA topological protein and critical for aging-related biological processes, such as DNA repair. RNA metabolism has been shown to be crucial in almost all biological processes, including aging, and many diseases, such as age-related degenerative diseases. However, none of eukaryotic topoisomerases have been linked to RNA metabolism. In collaboration with Dr. Weidong Wangs group, we identified Top3β as the first eukaryotic RNA topoisomerase, which is present in polyribosome and stress granule in the cell. We further demonstrated that Top3β interacts with Fragile X protein (FMRP) to regulate synaptic formation at the neuromuscular junction (NMJ) in Drosophila. FMRP is a major protein linked to Fragile X syndrome, a common form of intellectual disability, and autism. We have shown that Top3β and FMRP bind a number of common sets of mRNAs, including those encoded by genes with neuronal functions related to schizophrenia and autism. Top3β mutations have been shown to be associated with schizophrenia and intellectual disability in humans. These findings suggest Top3β acts as an RNA topoisomerase in RNA metabolism and interacts with FMRP in promoting neural development and mental health. This line of work has been published in Nature Neuroscience (2013). Demonstration of the first eukaryotic RNA topoisomerase will facilitate determining the role of RNA metabolism, especially topology, in aging and neurological diseases, which opens a novel line of research in the aging field. In summary, we have made significant progress towards understanding molecular mechanisms underlying aging and age-related diseases. We have developed a bioinformatic tool for high throughput functional studies of genomic data. We have identified the first RNA topoisomerase and demonstrated its role in maintaining mental health. These studies are valuable for advancing the objectives of the Translational Gerontology Branch and the mission of the NIA to understand the basic biology of aging and develop efficient interventions for humans.