3 Ways FFPE Technology is Used in Cancer Research

The challenge of finding high quality bio-specimens for cancer research is a huge issue, and there is limited availability of fresh tissue samples from patients in the quantities required for cellular research. The analysis of the protein pathways and cellular interactions in a tumor cell, as opposed to those of a normal cell, are essential to the understanding of the make-up of each cancer variant.

Recently, researchers have moved towards using formalin-fixed paraffin-embedded (FFPE) tissues in their research, as there are greater quantities of these available in tissue archives. However, there are many issues with the extraction of the cells, DNA and RNA from these fixed tissues. Here we summarize three different technologies that enable the use of FFPE tissues in cancer research.

Immunofluorescence imaging
In a recent study, the ability of PerkinElmer’s Vectra® multispectral imaging system and inForm data analysis software, for the analysis of control (tonsil) and clinical breast cancer FFPE samples using immunofluorescence labeling is demonstrated. Investigating signaling pathways involved in tumor progression is another important part of cancer research. Another study, using the Vectra® multispectral imaging system and inForm software, identifies the AKT, ERK, and S6 pathways in FFPE tissue sections.

RNA isolation
A recent publication in Cancer Research suggests that microRNAs (miRNAs) play a role in modulating expression of the protein special AT-rich sequence-binding protein 1 (SATB1) expression in ductual breast cancer. This protein is associated with a poor breast cancer prognosis, as it is an indicator of tumor metastasis. miRNAs were extracted from clinical FFPE samples of primary ductual breast cancer, using QIAGEN’s miRNeasy FFPE kit. Expression levels were analyzed using quantitative RT-PCR.

Flow cytometry isolation
A customer case study, based on research from the Translational Genomics Research Institute (TGen), outlines a flow cytometry-based method (using BD Biosciences BD Influx Cell Sorter) used to isolate pure populations of tumor cell nuclei solid tumor FFPE tissues, including triple negative breast carcinomas (TNBCs), glioblastomas, bladder carcinoma, and small cell carcinoma of the ovary. The group also developed a DNA extraction methodology compatible with Agilent’s Human Genome oligonucleotide array CGH kits and used whole exome sequencing analyses.

References:
doi: 10.1158/1538-7445.AM2014-5199
doi: 10.1371/journal.pone.0050586