A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression

Next-generation sequencing (NGS) can identify and validate new biomarkers of cancer onset, progression and therapy resistance. Substantial archives of formalin-fixed, paraffin-embedded (FFPE) cancer samples from patients represent a rich resource for linking molecular signatures to clinical data. However, performing NGS on FFPE samples is limited by poor RNA purification methods.

To address this hurdle, researchers from California State University Northridge developed an improved methodology for extracting high-quality RNA from FFPE samples. By briefly integrating a newly-designed micro-homogenizing (mH) tool with commercially available FFPE RNA extraction protocols, RNA recovery is increased by approximately 3-fold while maintaining standard A260/A280 ratios and RNA quality index (RQI) values. Furthermore, the researchers demonstrate that the mH-purified FFPE RNAs are longer and of higher integrity.

rna-seqA. FFPE samples are usually used for hematoxylin and eosin (H&E) and/or immunohistochemistry (IHC) stains. To overcome hurdles associated with gene expression analyses of tissue in FFPE samples, we show that the mH can increase the purification of high-quality RNA for downstream applications. B. H&E staining of the four xenograft FFPE samples (BxPC3 [B] and FG [F]) or patient (MDA-AC2 [M]) xenografts (S = subcutaneous, O = orthotopic).

Hoover M, Adamian Y, Brown M, Maawy A, Chang A, Lee J, Gharibi A, Katz MH, Fleming J, Hoffman RM, Bouvet M, Doebler R, Kelber JA. (2016) A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression between orthotopic and subcutaneous pancreatic cancer patient-derived xenografts. Oncotarget [Epub ahead of print]. [article]

Leave a Reply

Your email address will not be published. Required fields are marked *

*

Time limit is exhausted. Please reload CAPTCHA.