RNA-Seq considerations when working with nucleic acid derived from FFPE

RNA-seq from FFPE samples

Millions of formalin-fixed paraffin-embedded (FFPE) tissue sections are stored in oncology tissue banks and pathology laboratories around the world. Formalin fixation followed by embedding paraffin has historically been a popular preservation method in histological studies as morphological features of the original tissue remain intact. However for RNA-seq or other gene expression methods, formalin fixation and paraffin embedding can degrade and modify RNA, complicating retrospective analysis using this commonly used archival method.

During the fixation and embedding process RNA is affected in the following ways:

  1. Degradation of RNA to short ~100 base fragments as a result of sample treatment during fixation or long term storage in paraffin.
  2. Formaldehyde modification of RNA. Formaldehyde modification can block base pairing and can cause cross-linking to other macromolecules. These RNA modifications include hydroxymethyl and methylene bridge cross-links on amine moieties of adenine bases.
  3. High variability in the degree of RNA degradation and modification in FFPE samples precludes transcriptomic similarity and gene expression correlation studies, or simply forces researchers to exclude certain samples.
  4. Oligo-dT approaches are not recommended when amplifying RNA as most RNA fragments derived from FFPE no long contain a poly(A) tail making rRNA depletion a necessary first step prior to RNA-seq.

If formalin fixation and paraffin embedding can’t be avoided, Ahlfen et al., nicely summarize best practices for improving RNA quality and yield from FFPE samples. These include:

  1. Starting fixation and cutting samples into thin pieces to avoid tissue autolysis.
  2. Reduction of fixation time (< 24 hours) to reduce irreversible cross-linking and RNA fragmentation during storage of FFPE blocks.
  3. Utilizing a method to reverse cross-linking during RNA isolation. These include heating RNA to remove some formaldehyde cross-linking. Reaction of formaldehyde with amino groups in bases and proteins are largely irreversible and inhibit cDNA synthesis.
  4. Use of a rRNA depletion step and random priming as opposed to oligo-dT based reversed transcription.
  5. RNA QC methods such as a measurement of RNA integrity or one of several RT-PCR based kits to qualify a sample prior to RNA-seq.

Despite these challenges, FFPE samples are frequently used in transcriptomic studies and in many cases correlate nicely with fresh frozen samples (Hedegaard et al., 2014; Li et al., 2014; Zhao et al., 2014). The study of somatic mutations continues to remain a challenge in FFPE tissue due to fragmentation and the presence of artifacts. Nevertheless, RNA molecules from FFPE are being used regularly for investigating both non-coding and coding parts of the genome.

If you have FFPE blocks or total RNA and would like to perform gene expression analysis by RNA-Seq, we recommend you start with a NGS service provider who has specific experience with FFPE RNA isolation, QC, library preparation, sequencing and data analysis. Providers with this experience can be found using this search on Genohub: https://genohub.com/ngs/?r=mt3789#q=4c5f2d036f.

 

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