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
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.
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