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Updated: Feb 6, 2026

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
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Published on: August 21, 2016

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Nonfouling, Encoded Hydrogel Microparticles for Multiplex MicroRNA Profiling Directly from Formalin-Fixed,

Maxwell B Nagarajan1, Augusto M Tentori1, Wen Cai Zhang2

  • 1Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.

Analytical Chemistry
|August 15, 2018
PubMed

Insights

We developed a simple method to directly measure microRNAs (miRNAs) in formalin-fixed cells and tissues. This technique offers a faster, more sensitive way to analyze miRNA biomarkers in challenging FFPE samples.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biomarker Discovery

Background:

  • MicroRNAs (miRNAs) are crucial noncoding RNAs implicated in various diseases, including cancer.
  • Dysregulated miRNAs show potential as stable biomarkers due to their resilience.
  • Formalin-fixed, paraffin-embedded (FFPE) tissues are common but challenging for biomolecule extraction.

Purpose of the Study:

  • To develop a simplified protocol for direct miRNA measurement from FFPE tissues.
  • To overcome challenges associated with FFPE sample preparation and analysis.
  • To enable sensitive, quantitative, and multiplexed miRNA detection in FFPE samples.

Main Methods:

  • Fabrication of encoded hydrogel microparticles using stop-flow lithography.
  • Direct measurement of miRNA from formalin-fixed cells and FFPE tissue sections.
  • Comparison of miRNA levels with and without paraffin removal from FFPE tissues.

Main Results:

  • The microparticle assay demonstrated agreement between formalin-fixed and fresh cells.
  • FFPE tissue miRNA measurement with paraffin was 10% lower than without paraffin.
  • Differential miRNA signals were observed between normal and tumor FFPE tissues, identifying oncogenic and tumor-suppressing miRNAs.

Conclusions:

  • The developed protocol simplifies miRNA measurement from FFPE tissues.
  • This method reduces assay time and the need for hazardous chemicals.
  • It provides a sensitive, quantitative, and multiplexed approach for miRNA biomarker analysis in FFPE samples.

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