Superior Pathology

DNA and RNA Extraction from FFPE Tissue

Biomedical research frequently involves long-term studies, making tissue sample preservation essential for further advancements. Formalin-fixed paraffin-embedded (FFPE) tissue is a widely used preservation technique that continues to provide groundbreaking biological insights. This preservation method maintains the tissues’ integrity over an extended length of time and allows for the extraction of multiple sections from a single block. However, researchers face particular complexities when attempting to extract genetic material from FFPE samples. Continue reading to discover the process and understand the special care taken in order to isolate RNA and DNA samples without damaging the material in the process.

Diagram showing DNA molecules

FFPE DNA Extraction, A Slice of Innovative Biomedical Research

FFPE DNA extraction is a sensitive procedure and a trusted practice that holds immense significance in various fields, including cancer research, genetic studies, and forensic investigations. These archived tissue samples offer valuable insights into disease progression, biomarker discovery, and therapeutic plans. The FFPE preservation method was established in the late 1800s, and according to SageJournal’s Journal of Histochemistry & Cytochemistry, DNA extraction from FFPE samples began in the late 1900s. Since then, researchers have taken calculated action to optimize extraction protocols to obtain high-quality genetic material from FFPE samples. The practice has become essential in advancing biomedical research and clinical diagnostics.

Once the genetic material is extracted from the FFPE section, researchers are faced with multiple hurdles to preserve the sample before it succumbs to deterioration. Formalin-induced cross-links and RNase (äreˈnās), enzymes that break down RNA into smaller molecules, exacerbate the molecule’s inherent instability and susceptibility to degradation. To overcome such obstacles, RNA extraction protocols for FFPE samples incorporate methods to reverse cross-links, mitigate RNase activity, and preserve sample integrity.

Overcoming The Challenges of FFPE DNA Extraction

Traditional DNA extraction methods often fail to efficiently recover intact DNA stored for long-term use in FFPE samples without damaging the strands. However, specialized protocols tailored to FFPE tissue have proven to promote the longevity of extracted samples. Heat-induced antigen retrieval is a common pre-treatment step that involves incubating the FFPE tissue sections to maintain their integrity and reverse formalin-induced cross-links.

After incubation, the nucleic acids have been exposed, but the presence of enzymes like RNase often prohibits extraction at this point. Utilize proteases, enzymes that break the peptide bonds of proteins, or proteinase K, to remove any remaining enzymes that could damage your sample. This enzymatic digestion helps break down proteins and release DNA from the cross-linked matrix. If any remaining enzymes are present, samples are oftentimes bound to silica-based columns; fragments of the sample can be isolated using magnetic beads, reducing damage while residual contaminants are removed to complete the process.

Advancements in FFPE RNA Extraction Techniques

Advancements in FFPE RNA extraction techniques have significantly improved the efficiency and reliability of isolating high-quality RNA from archived tissue samples. These advancements address the challenges posed by formalin fixation and degradation, allowing researchers to unlock valuable genetic information stored within FFPE specimens. One notable advancement is the development of specialized extraction kits tailored specifically for FFPE samples. These kits often incorporate innovative reagents and protocols designed to optimize RNA recovery while minimizing sample breakdown.

4 Steps For Successful FFPE RNA Isolation

In addition to the specialized extraction protocols that have revolutionized FFPE RNA isolation, several key considerations must be addressed to ensure optimal results.

  • Sample Quality: The quality of an FFPE RNA isolation often reflects the quality of the original FFPE sample. Assess FFPE sample quality, including tissue fixation duration and storage condition. This crucial step could determine your extraction success. By ordering from a reputable biobank, you can trust the quality of your samples and set your research up for success.
  • Pre-treatment: Tailor pre-treatment steps, such as antigen retrieval and enzymatic digestion, based on sample characteristics to enhance nucleic acid recovery. Different sample characteristics, such as tissue type, age, and preservation method, can affect nucleic acid recovery. For example, heterogeneous samples, like tumors, often need customized protocols to ensure a representative analysis. 
  • RNase Barrier: Incorporate RNase inhibitors throughout the extraction process to safeguard RNA integrity and prevent decay.
  • Quality Control: Implement rigorous quality control measures, such as spectrophotometric analysis–to determine the concentration of DNA and RNA molecules–and PCR-based assays–to determine the presence of pathogens. These tests can be used to validate the integrity, purity, and success of the FFPE RNA isolation.


Unlock the Biomedical Secrets of FFPE Tissue Samples with Superior BioDiagnostics

DNA and RNA extracted from FFPE tissue offer a vital gateway to uncovering the genetic mysteries concealed within archived samples. The recovery of high-quality genetic material from FFPE samples has been transformed by creative extraction techniques despite the difficulties presented by formalin fixation. By adopting specialized methods, researchers will overcome challenges, enable the leverage of the abundant data in FFPE tissue, and propel progress in biomedical research and clinical practice.

Order your FFPE human tissue samples directly from Superior BioDiagnostics to pave the way for transformative discoveries and shape the future of medicine and molecular biology. Contact Superior BioDx–the biobank of choice for top-rated academic institutions–today and launch your research to the future with top-quality FFPE human samples.