Functional Genomic Study of Aging and Aging Interventions

衰老是一个生物学过程，其特征在于各种生理功能的逐渐衰退。有许多与年龄有关的变化，包括基因表达的变化，这些变化在酵母、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共享。老龄化领域的一个重要问题是这些与年龄有关的变化是否以及如何调节健康寿命和寿命。 无脊椎动物模型，包括C。elegans和D.黑腹果蝇是确定衰老过程的分子机制的最前沿研究。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，通常短于几个月，便于跟踪它们的整个生命，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。我们已经总结了无脊椎动物模型在衰老研究中的重要性，在一篇发表于Ageing Research Reviews（2013）的综述论文中。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。这些出版物将为无脊椎动物的衰老研究提供有价值的指导，特别是C。elegans和D.黑腹菌 像许多其他生物一样，衰老与两个强大的无脊椎动物模型中数千个基因的表达变化有关，C。elegans和D.黑腹菌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见解。解决这一问题的一种方法是确定哪些分子变化在C. elegans和D.黑腹菌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主要基于序列同源物来鉴定保守基因和蛋白质，但工具限于鉴定具有低序列相似性但功能保守的基因和蛋白质，后者可能由基因组的显著部分组成。为了解决这个问题，我们与Kevin Becker和Ilya Goldberg博士领导的几个内部小组合作，开发了一种生物信息学工具，用于C. elegans和D.黑腹菌 我们已经证明了这些基因集在复杂生物表型（包括衰老）的系统生物学研究中的实用性。这一系列的工作已经发表在BMC Genomics 2013上。本文所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体中的大量基因组数据，并在未来的研究中促进对各种生物过程（如衰老）中功能保护的研究。 在与衰老过程相关的保守蛋白中，拓扑异构酶是已知的解决DNA拓扑蛋白所必需的，并且对于与衰老相关的生物过程（例如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至关重要，包括衰老和许多疾病，如与年龄相关的退行性疾病。然而，没有真核拓扑异构酶与RNA代谢有关。本课题组与王卫东博士研究组合作，首次发现Top3是真核生物中的第一个RNA拓扑异构酶，存在于细胞内的多聚核糖体和应激颗粒中。我们进一步证明了Top3与脆性X蛋白（FMRP）相互作用，以调节果蝇神经肌肉接头（NMJ）的突触形成。FMRP是与脆性X综合征（一种常见的智力残疾和自闭症）相关的主要蛋白质。我们已经证明Top3和FMRP结合了许多常见的mRNA集，包括那些由与精神分裂症和自闭症相关的神经元功能基因编码的mRNA。Top3突变已被证明与人类精神分裂症和智力残疾有关。这些发现表明Top3在RNA代谢中作为RNA拓扑异构酶，并与FMRP相互作用以促进神经发育和心理健康。这一系列的工作已经发表在Nature Neuroscience（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，这为衰老领域的研究开辟了一条新的道路。 总之，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生物信息学工具，用于基因组数据的高通量功能研究。我们已经确定了第一个RNA拓扑异构酶，并证明了它在维持心理健康中的作用。这些研究对于推进翻译老年学分支的目标和NIA的使命是有价值的，即了解衰老的基本生物学并为人类开发有效的干预措施。

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.