PIXUL-FFPE: High throughput platform for chromatin and DNA sample preparation from formalin fixed paraffin embedded (FFPE) tissue samples- supplement application.

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Formalin-fixed paraffin-embedded (FFPE) tissue archives represent the largest clinically annotated human specimen repository. The estimated millions of available FFPE tissue samples provide a vast resource for the discovery of disease epigenetic pathways, biomarkers and drug targets. And yet, these samples are highly underutilized because current methods for extracting molecular information from FFPE samples are slow, inefficient, labor-intensive, insufficiently sensitive to detect gene-bound enzymes (drug targets) and have low throughput to fully exploit their enormous research and clinical potential. There is an unmet need for better tools to take advantage of these archived clinical samples to retrieve chromatin, RNA, DNA and proteins for the discovery of biomarkers for personal medicine. We have previously developed and marketed a high-throughput PIXUL sonicator which generates high-intensity focused ultrasound (HIFU) in wells of 96-well microplate to advance chromatin, RNA, DNA and protein preparation from cultured cells and tissues. As proposed in our current Fast Track STTR application (now in year 2 of Phase 2), we have established protocols for extraction of chromatin, DNA, and RNA from FFPEs using PIXUL. We have benchmarked these FFPE retrieval protocols against matched mouse frozen tissues (brain, heart, kidney and liver) using microplate Matrix-ChIP-qPCR/seq, Matrix-MeDIP-qPCR/seq, Matrix-RT-qPCR/seq platforms. Still, test-tubes and heat block are necessary for heat retrieval of analytes. The process can be simplified if all the sample preparation steps, including sonication and heating, are done in one instrument using the same 96-well microplate. Thus, an important goal of the current STTR grant was to engineer a more versatile PIXUL instrument for processing FFPEs. Accordingly, we designed a 96-well microplate dual functionality laboratory PIXUL iteration instrument that allows to program ultrasound and heating/cooling parameters, PIXUL H&C. The library preparation, sequencing kits and PIXUL engineering costs are still limiting our ability to optimize and commercialize PIXUL H&C for high throughput analysis of tissues including FFPEs. The administrative supplement is requested to expedite PIXUL-FFPE R&D by increasing the number of tissues for NGS testing and allowing more engineering resources to develop PIXUL H&C commercial prototype and custom microplates. Genome-wide tissue multiomic studies have provided valuable resources for discoveries. Thus, the high- throughput, fast and efficient user-friendly dual-function PIXUL H&C device that we propose to optimize for NGS applications and to commercialize will demonstrate its utility to researchers as an important means to interrogate the vast repositories of FFPEs to discover disease pathways, candidate biomarkers and drug targets. Given that FFPE are most often used in clinical laboratories for testing molecular biomarkers we expect that PIXUL H&C, alike PCR machines, will also have wide use in clinical settings.