SBIR: Technology for Overcoming Bottlenecks in Chromatin Extraction from Challenging Biological Samples

PROJECT SUMMARYThe complex organization of chromatinDNA with its associated nuclear proteinsis closely tied to the regulation of gene expressionand evidence points to a central role for chromatin deregulation in tumor developmentA common analysis of chromatin regulatory protein localization is the chromatin immunoprecipitationChIPassaywhich involves crosslinking of proteins to DNAfollowed by chromatin fragmentationand then antibody mediated immunoprecipitation of the DNA fragmentsSubsequent quantificationquantitative PCR or Next Generation Sequencingis usually performedThis assay is a key tool for both industry and academic research studying cancer related epigeneticsThe challenge is that the formaldehyde crosslinks render the chromatin resistant to mechanicali eacoustic sonicationlysismaking current fragmentation techniques inefficient and time consumingFurthermorethese techniques result in high sample to sample variability and require high powerlowthroughputand expensive sonication devicesOur customer discovery interviews have highlighted these pain pointsthere 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 applicationsTriangle Biotechnology recently developed a unique cavitation enhancing reagentRapidShearthat substantially improves the efficiency of acoustic fragmentation of genomic DNAHoweverthis reagent formulation shows little to no improvement for chromatin fragmentation from fixed cellsTo address the aforementioned sample preparation challenges in the epigenetics spacewe are developing a new reagentMegaSheara more aggressive formulation for acoustic cavitation enhancement designed specifically for chromatin processingPreliminary studies indicated that MegaShear facilitates a substantial improvement in chromatin fragmentation throughputconsistencyand yieldValidation and optimization of this technology will alleviate a critical bottleneck in the ChIP workflowMegaShear will enable a substantial leap in high quality sample preparation throughput desired by large companiesas well as an increase in accessibility by enabling the use of low cost sonicatorsdesired by small academic labsWith this SBIRwe will demonstrate proof of concept for MegaShearvalidating the ability to produce high quality chromatin with high consistencyreducing capital equipment costand substantially increasing throughputSuccess of this project will enable a novel commercial solution for addressing market pain points in chromatin analysis RELEVANCE TO PUBLIC HEALTHGrowing evidence points to a central role for chromatin deregulation in tumor developmentand assays such as the chromatin immunoprecipitationChIPassay are key tools for both industry and academic research in cancer related epigeneticsHoweverissues with consistency and throughput have severely limited the utility and adoption of ChIP for personalized medicine applicationsTo solve this problemTriangle Biotechnology has developed MegaSheara cavitation enhancement reagent with applications for biological sample dispersion and chromatin fragmentationMegaShear can significantly decrease sample processing time and substantially increase throughputeliminating the barriers in chromatin analysis and enabling robusthigh throughput biological sample processing for ChIP and other epigenetic assays