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

项目摘要 越来越多的人认识到表观遗传调节机制在正常人和正常人中的重要性。 发展和疾病。染色质结构的动态调节是一个经常研究的中心问题， 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， 智力残疾、自闭症和癫痫等多种发育综合征， 大约50%的人类癌症，其中许多被认为是多种多样的驱动突变， 肿瘤的然而，许多用于研究染色质生物学的测定仍然是繁琐的、昂贵的，或不稳定的。 缺乏实验的鲁棒性，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 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，可以大大减少时间和声学 超声处理装置中基因组DNA片段化所需的能量。这项建议旨在扩大 应用我们的空化增强技术来解决科学相关的挑战， 高质量的染色质。长时间甲醛固定（FF），然后脱水， 石蜡包埋（PE）是存档组织样本的标准方法。这些FFPE组织收集 包含了大量关于人类疾病的信息。然而，从这些标本中提取染色质， 事实证明，这几乎是不可能的，因为保存相关的DNA-蛋白质相互作用的挑战。初步 数据表明，我们的空化增强试剂具有简化和标准化染色质的潜力 从存档组织中提取，从而大大扩展了FFPE衍生染色质的应用范围 基于表观遗传学的生物医学研究。

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.