Development of a cavitation enhancement technology to access archived tissues for epigenetic-based biomedical research

项目摘要 越来越多的人意识到表观遗传调控机制在正常人类中的重要性 发展和疾病。染色质结构的动态调控是一个研究较多、研究较多的核心问题 表观遗传过程。染色质相关蛋白的突变与神经系统疾病有关 如智力残疾、自闭症和癫痫，以及各种发育综合征，并在 大约50%的人类癌症，其中许多被认为是多种不同 肿瘤。然而，许多用于研究染色质生物学的分析方法仍然繁琐、昂贵或 缺乏实验的稳健性，这些问题导致我们对这一关键问题的理解存在很大差距 生物机制。因此，创新的新技术使高效和可再生 我们迫切需要对表观遗传机制进行研究。 我们发明了一种独特的空化增强剂，大大减少了时间和声学 在超声设备中进行基因组DNA碎裂所需的能量。这项建议旨在扩大 应用我们的空化增强技术来应对开采的科学相关挑战 档案组织中的高质量染色质。长时间甲醛固定(FF)，然后脱水和 石蜡包埋(PE)是存档组织样本的标准方法。这些FFPE组织收藏品 包含了关于人类疾病的丰富信息。然而，从这些标本中提取染色质 事实证明，由于保存相关DNA-蛋白质相互作用的挑战，这几乎是不可能的。初步 数据表明，我们的空化增强剂有可能简化和标准化染色质 从存档组织中提取，从而大大扩大了FFPE来源的染色质的应用范围 以表观遗传学为基础的生物医学研究。

Project Summary There is a growing appreciation for the importance of epigenetic regulatory mechanisms in both normal human development and disease. The dynamic regulation of chromatin architecture is a frequently studied and central epigenetic process. Mutations in chromatin-associated proteins have been linked to neurological disorders such as intellectual disability, autism, and epilepsy, a variety of developmental syndromes, and detected in approximately 50% of human cancers, many of which are recognized as driver mutations across multiple diverse tumors. Nevertheless, many of the assays used to study chromatin biology remain cumbersome, expensive, or lack experimental robustness, problems which have resulted in large gaps in our understanding of this critical biological mechanism. Therefore, innovative new technologies that enable efficient and reproducible interrogation of epigenetic mechanisms are badly needed. We have invented a unique cavitation enhancement reagent that dramatically decreases the time and acoustic energy required for genomic DNA fragmentation in a sonication device. This proposal aims to expand the application of our cavitation enhancement technology to address the scientifically relevant challenge of extracting high quality chromatin from archival tissues. Lengthy formaldehyde fixation (FF) followed by dehydration and paraffin embedding (PE) is the standard method of archiving tissue samples. These FFPE tissue collections contain a wealth of information on human disease. However, extraction of chromatin from these specimens has proven virtually impossible because of the challenge of preserving relevant DNA-protein interactions. Preliminary data suggest that our cavitation enhancement reagent has the potential to simplify and standardize chromatin extraction from archived tissues, thereby greatly expanding the range of applications for FFPE-derived chromatin in epigenetic-based biomedical research.