The application of Enhanced Cavitation to enable DNA and Chromatin Extraction from Archived Tissues


Year of Award:
2017
Award Type:
R33
Project Number:
CA206939-01A1
RFA Number:
RFA-CA-16-004
Technology Track:
Biospecimen Science Technologies
PI/Project Leader:
PATTENDEN, SAMANTHA GAIL (contact);
Other PI or Project Leader:
DAVIS, IAN J; DAYTON, PAUL A
Institution:
UNIV OF NORTH CAROLINA CHAPEL HILL
ABSTRACT / PROJECT SUMMARY Formalin-fixed paraffin embedded (FFPE) patient biopsy samples represent an important source of tumor tissue for cancer research. FFPE samples can be used to extract DNA for analyzing tumor-specific gene mutations and for cancer diagnostics. There is considerable interest in expanding the use of FFPE tissue to include analysis of tumor epigenetics, which are heritable modifications not associated with alteration of DNA sequence. Changes in the signature of chromatin, which consists of DNA, histone and other nuclear proteins, are early epigenetic events in a wide variety of cancers. Therefore, scientists and clinicians are interested in developing therapeutics and diagnostics around tumor-specific chromatin signatures. Currently, there is no method available to extract chromatin from FFPE samples that is appropriate for all types of chromatin analysis methods. We have invented a unique chemically inert reagent based on a perfluorocarbon nanodroplet suspension that can be used to enhance and simplify the extraction of chromatin from FFPE tissue. These nanodroplets can be prepared in sub-micron form, which makes them nearly neutrally buoyant and more likely to impregnate intracellular spaces to enhance tissue dispersion. We will optimize the formulation for the nanodroplet reagent and validate its use in a unique single-step protocol to extract chromatin from rodent xenograft and human FFPE tumor biopsy samples. We hypothesize that this unique reagent will enable detection of clinically meaningful chromatin signatures from FFPE tumor tissue potentially enabling, for the first time, the development of chromatin-based cancer diagnostics.