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

Formalin fixed paraffin embeddedFFPEtissue archives represent the largest clinically annotated human specimen repositoryThe estimated millions of available FFPE tissue samples provide vast resource for the discovery of disease epigenetic pathwaysbiomarkers and drug targetsAnd yetthese samples are highly underutilized because current methods for extracting molecular information from FFPE samples are slowlabor intensiveinsufficiently sensitive to detect gene bound enzymesdrug targetsand have low throughput to fully exploit their enormous research and clinical potentialThere is an unmet need for better tools to take advantage of these archived clinical samples to retrieve chromatin and DNA for the discovery of epigenetic biomarkers for personal medicineThe chromatin immunoprecipitationChIPassaya widely used approach for identifying genomeassociated proteins or DNA modificationsis one of the most powerful tools used in epigenetic studiesTo facilitate chromatin analysiswe have developed a high throughput microplate based Matrix ChIP qPCR platform and engineered a device for fast chromatin shearing which uses an array ofminiature ultrasound transducers PIXULPIXelated ULtrasoundExtraction of chromatin from FFPE samples is a multistep process which includes chromatin shearingUltrasound facilitates chromatin extraction from FFPE samplesThe goal of this Matchstick Fast Track STTR projectworking with UW partner laboratoriesis to develop and validate a user friendly and efficient high throughout PIXUL based technologyPIXUL FFPEto extract and shear chromatin and DNA from small FFPE samples for epigenetic analysis for use in the research market paving the way for use in clinical settingsThe following aims are proposedIn AimPhaseWe will design and validate custom PIXULwell microplate for more efficient extraction of chromatin and DNA from FFPE tissue samplesIn AimPhasewe will optimize PIXUL FFPE protocol for fast and high throughput chromatin extraction from small FFPE samples while maximizing sample integrityIn AimPhasewe will demonstrate the translational utility of PIXUL FFPE by comparative ChIP analysis of matched pairs of fresh frozen and FFPE glioblastomaGBMtumor sectionsIn AimPhasewe will modify PIXUL instrument for extraction of chromatin from FFPE samplesSearch for epigenetic therapies has slowed down by paucity of available dataThusintegrating the customwell plates and improved protocol with the modified PIXUL instrument will greatly increase utilization of FFPE specimens in the research market place attracting greater numbers of investigators to explore the vast repositories of archived human tissues and as such advancing precision medicine The vast repositories of formalin fixed paraffin embeddedFFPEtissue represent enormous resource for discoveries of epigenetic biomarkersdisease pathways and drug targetsAnd yetthese samples remain largely underutilized because the methods for extraction of chromatin from FFPE for epigenetic analysis are inefficientWe have demonstrated the value of ultrasound for chromatin retrieval from FFPE samplesThis proposal addresses the need to develop high throughput and sensitivity technologyultrasound based PIXUL FFPEfor recovery of soluble chromatin from FFPE samples