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.
Formalin-fixed paraffin embedded (FFPE) patient biopsy samples are an important source of tumor tissue for cancer research and diagnostics. There is considerable interest in expanding the use of FFPE tissue to include epigenetic cancer signatures, which are heritable changes not associated with alteration in DNA sequence. We have invented a chemically inert reagent based on a metastable perfluorocarbon nanodroplet that our preliminary data indicate can be used to enhance and simplify processing of FFPE tissue for epigenetic analyses, including cancer diagnostics. We will explore and optimize aspects of this novel approach, with a goal towards commercial translation.
| Chiarella, Anna M; Quimby, Austin L; Mehrab-Mohseni, Marjan et al. (2018) Cavitation Enhancement Increases the Efficiency and Consistency of Chromatin Fragmentation from Fixed Cells for Downstream Quantitative Applications. Biochemistry 57:2756-2761 |
