How scientists are extracting molecular secrets from decades-old tissue libraries through systematic comparison of FFPE RNA extraction kits
For over a century, hospitals worldwide have been preserving tissue samples in a special way: fixing them in formalin and embedding them in paraffin wax. These FFPE (formalin-fixed, paraffin-embedded) samples represent an irreplaceable treasure trove for medical research, with over a billion specimens stored in archives globally 1 . They are the cornerstone of cancer diagnostics and research, yet they present a formidable challenge to scientists trying to extract genetic information from them. This article explores the meticulous science behind unlocking high-quality RNA from these precious time capsules of human disease.
The ability to extract quality RNA from these samples has become increasingly important with advances in RNA sequencing (RNA-seq) technologies. High-quality RNA enables researchers to identify gene fusions in cancer, understand treatment resistance, and discover new therapeutic targets 2 .
With the growing importance of FFPE samples in molecular research, particularly in oncology, many commercial companies have developed specialized kits designed to tackle the unique challenges of FFPE RNA extraction. While laboratories sometimes develop their own custom protocols, commercially available kits remain popular because they offer standardized, reproducible methods 1 .
Researchers evaluated both quantity and quality using precise measurements 1 :
Seven commercial kits evaluated 5 :
The extensive comparison revealed striking differences in kit performance. While all kits successfully extracted RNA, their effectiveness varied significantly.
| Extraction Kit | Quantity | Quality | Best Application |
|---|---|---|---|
| ReliaPrep (Promega) | Excellent | Very Good | When maximizing yield is critical |
| High Pure (Roche) | Good | Excellent | When quality is the top priority |
| PureLink (Thermo Fisher) | Very Good | Excellent | Balanced needs with appendix tissues |
| AllPrep (QIAGEN) | Moderate | Moderate | When both DNA and RNA are needed |
In a crucial test that multiplied relative yield by DV200 to create a combined "quality × quantity" score, the ReliaPrep FFPE Total RNA Miniprep System (Promega) significantly outperformed all other kits 5 . This suggests that while the Roche kit delivers superior consistency, the Promega kit offers the best balance of both quantity and quality for the tested tissue samples 1 .
Uses optimized lysis conditions and purification chemistry to deliver high yields of quality RNA 5 .
Employs specialized buffers and purification columns to consistently recover high-quality RNA 5 .
Simultaneously purifies both DNA and RNA from the same sample 4 .
Utilizes proprietary CAT5 catalytic technology to chemically reverse formaldehyde crosslinks 6 .
Excels with low-input samples (as little as 10ng total RNA) 7 9 .
Effectively removes ribosomal RNA, crucial for FFPE samples 7 .
Employs Adaptase technology to work with a broad range of RNA inputs 9 .
Adaptations for FFPE tissues are opening new frontiers 2 .
Billions of archived samples will continue to yield molecular secrets.
The next time you hear about a breakthrough in cancer research that utilized historical tissue samples, remember the meticulous science of RNA extraction that made it possible—where choosing the right kit can determine whether hidden genetic secrets remain locked away or reveal transformative insights into human disease.