Development of nanodroplet enhanced ultrasonic cavitation technologyto enable the study of chromatin accessibility in FFPE tissues

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Abstract Triangle Biotechnology is developing ChromExtract™, a low-cost, nanodroplet-based sonication reagent for chromatin extraction from formalin-fixed paraffin-embedded (FFPE) tissues for downstream chromatin profiling and chromatin accessibility analyses. These techniques are central to epigenomic research and mapping of histone modifications, enhancers, and chromatin states, enabling systematic investigation of epigenomic effects on cell identity, development, lineage specification, and disease. While chromatin profiling analyses have been used for over two decades, several bottlenecks exist that have prevented epigenetic profiling from yielding consistent and reliable data from FFPE tissues, most notably the poor quality and yield associated with current chromatin extraction methods. This is a considerable problem, as most translational research and clinical diagnostics employ FFPE tissue specimens. Moreover, compatibility with FFPE tissues provides access to a massive bank of archival samples that can be used to further characterize molecular subtypes for pathologies of interest. Given the current state of the field, a rapid, high-yield, and high-efficiency method for extraction of chromatin from FFPE tissue that results in improved chromatin quality and standardization across sample types would have a significant impact on the field and potential applications for studying chromatin accessibility and other epigenetic assays in medical research. There are currently no commercially available solutions for analyzing chromatin accessibility in FFPE tissue samples. This type of analysis employs a non-targeted approach to systematically query open regions of chromatin associated with gene expression, allowing researchers to broadly understand how changes in chromatin state affect disease progression independent of alterations in specific histone marks or transcription factor distribution. Triangle’s ChromExtract provides a workflow that employs an extracellular matrix (ECM)-digesting enzyme cocktail followed by enhanced sonication using a low-cost, perfluorocarbon (PFC) nanodroplet-based reagent for high-quality, high-yield, and consistent chromatin extraction from FFPE tissue in any commercially available sonicator. In this Phase I SBIR project, Triangle Bio will: 1) Demonstrate enhanced cavitation and increased resilience of nanodroplet formulation in FFPE-based lysis buffers and 2) Optimize and validate the FFPE tissue chromatin extraction workflow for Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) seq. This work will establish the feasibility of commercializing ChromExtract by demonstrating the ability to enable NGS-based analysis of chromatin extracted from FFPE samples, producing results that are rigorous, reproducible, efficient, and cost effective. This will be followed in a future Phase II application by further validation with other downstream NGS-based workflows.