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

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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.