Friday, November 22, 2024
11/22/2024
PROJECT SUMMARY The complex organization of chromatin (DNA with its associated nuclear proteins) is closely tied to the regulation of gene expression, and evidence points to a central role for chromatin deregulation in tumor development. A common analysis of chromatin regulatory protein localization is the chromatin immunoprecipitation (ChIP) assay, which involves crosslinking of proteins to DNA, followed by chromatin fragmentation, and then antibody mediated immunoprecipitation of the DNA fragments. Subsequent quantification (quantitative PCR or Next Generation Sequencing) is usually performed. This assay is a key tool for both industry and academic research studying cancer-related epigenetics The challenge is that the formaldehyde crosslinks render the chromatin resistant to mechanical (i.e. acoustic sonication) lysis, making current fragmentation techniques inefficient and time-consuming. Furthermore, these techniques result in high sample-to-sample variability and require high-power, low- throughput, and expensive sonication devices. Our customer discovery interviews have highlighted these pain points; there is an urgent need for a higher quality and higher throughput method of chromatin fragmentation before assays such as ChIP can be incorporated into cancer diagnostics applications. Triangle Biotechnology recently developed a unique cavitation enhancing reagent (RapidShear) that substantially improves the efficiency of acoustic fragmentation of genomic DNA. However, this reagent formulation shows little to no improvement for chromatin fragmentation from fixed cells. To address the aforementioned sample preparation challenges in the epigenetics space, we are developing a new reagent, MegaShear, a more aggressive formulation for acoustic cavitation enhancement designed specifically for chromatin processing. Preliminary studies indicated that MegaShear facilitates a substantial improvement in chromatin fragmentation throughput, consistency, and yield. Validation and optimization of this technology will alleviate a critical bottleneck in the ChIP workflow. MegaShear will enable a substantial leap in high quality sample preparation throughput desired by large companies, as well as an increase in accessibility by enabling the use of low-cost sonicators, desired by small academic labs. With this SBIR, we will demonstrate proof of concept for MegaShear, validating the ability to produce high quality chromatin with high consistency, reducing capital equipment cost, and substantially increasing throughput. Success of this project will enable a novel commercial solution for addressing market pain points in chromatin analysis.
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