MicroRNAs (miRNA) are short non-coding RNAs that have been implicated in many diseases, including cancers, and show promise as highly stable biomarkers. Formalin-fixed, paraffin-embedded (FFPE) tissue is a valuable sample type to assay for biomolecules because it is a convenient storage method and is often used by pathologists for staining. However, extracting biomolecules from FFPE tissue is challenging because of the presence of cellular and extracelullar proteins, formaldehyde crosslinks, and paraffin. Moreover, most protocols to measure miRNA in FFPE tissue are time-consuming and laborious. Here, we report a simple protocol to directly measure miRNA from formalin-fixed cells and FFPE tissue sections using hydrogel microparticles with nucleic acid probes (Fig. 1). Measurements by these particles of formalin-fixed cells and fresh cells agree quantitatively, and measurements of FFPE tissue with paraffin show about 10% losses compared to FFPE tissue when paraffin is removed before the assay (Fig. 2). This new approach reduces assay times, reduces the use of hazardous chemicals to remove paraffin, and provides a quantitative and multiplexed measurement of miRNA in FFPE tissue.

Non-fouling, encoded hydrogel particles for multiplex microRNA profiling directly from formalin-fixed paraffin embedded tissue

256th National Meeting (2018)

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