RNA study from FFPE

Formalin-fixed paraffin-embedded (FFPE) tissue is the most common tissue specimen widely available. Moreover, long clinical follow-up is on hand.

Therefore, FFPE material is a precious source of material for identifying predictive and/or prognostic biomarkers in cancer research on the basis of gene expression. However, the main drawback of FFPE tissue is the significant reduction in quantity and quality of the extracted RNA.

The aim of this study is the comparison of different commercially available kits for the RNA isolation in FFPE tissue material.

Altogether, on the basis of the number of adequate isolations, the kit from Qiagen seems to be the most appropriate kit to be used in our further studies that require RNA isolation from FFPE material. (22089347)

Types

 expression profiling from FFPE
 RT-PCR from FFPE

• qRT-PCR from FFPE

By genes

 HMGA2 expression from FFPE (21532495)
 ER (estrogen receptor) (21326033)
 PR (progesterone receptor) (21326033)
 HER2 (21326033)

References

 Expression Analysis on Archival Material: Comparison of 5 Commercially Available RNA Isolation Kits for FFPE Material. Boeckx C, Wouters A, Pauwels B, Deschoolmeester V, Specenier P, Lukaszuk K, Vermorken JB, Pauwels P, Peeters M, Lardon F, Baay MF. Diagn Mol Pathol. 2011 Dec;20(4):203-11. PMID: 22089347

 HMGA2 expression analysis in cytological and paraffin-embedded tissue specimens of thyroid tumors by relative quantitative RT-PCR. Jin L, Lloyd RV, Nassar A, Lappinga PJ, Sebo TJ, Swartz K, Seys AR, Erickson-Johnson MR, Roth CW, Evers BR, Oliveira AM, Zhang J. Diagn Mol Pathol. 2011 Jun;20(2):71-80. PMID: 21532495

 Quantitative determination of estrogen receptor, progesterone receptor, and HER2 mRNA in formalin-fixed paraffin-embedded tissue—a new option for predictive biomarker assessment in breast cancer. Müller BM, Kronenwett R, Hennig G, Euting H, Weber K, Bohmann K, Weichert W, Altmann G, Roth C, Winzer KJ, Kristiansen G, Petry C, Dietel M, Denkert C. Diagn Mol Pathol. 2011 Mar;20(1):1-10. PMID: 21326033

 Analytical performance of a qRT-PCR assay to detect guanylyl cyclase C in FFPE lymph nodes of patients with colon cancer. Beaulieu M, Desaulniers M, Bertrand N, Deschesnes RG, Beaudry G, Garon G, Haince JF, Houde M, Holzer TJ. Diagn Mol Pathol. 2010 Mar;19(1):20-7. PMID: 20186008

 Optimized protocol for gene expression analysis in formalin-fixed, paraffin-embedded tissue using real-time quantitative polymerase chain reaction. Votavova H, Forsterova K, Stritesky J, Velenska Z, Trneny M. Diagn Mol Pathol. 2009 Sep;18(3):176-82. PMID: 19704263

 Multiple gene expression analyses in human lymphoid tissues by taqman low-density array using amplified rna isolated from paraffin-embedded samples. Gloghini A, Canal B, Dal Maso L, Carbone A. Diagn Mol Pathol. 2009 Sep;18(3):156-64. PMID: 19704261

 Improved diagnostic segregation of mantle cell lymphoma by determination of cyclin D1/D3 expression ratio in formalin-fixed tissue. Mangseth K, Helgeland L, Klos J, Molven A, Vintermyr OK. Diagn Mol Pathol. 2009 Sep;18(3):150-5. PMID: 19704260

 Effects of processing delay, formalin fixation, and immunohistochemistry on RNA Recovery From Formalin-fixed Paraffin-embedded Tissue Sections. van Maldegem F, de Wit M, Morsink F, Musler A, Weegenaar J, van Noesel CJ. Diagn Mol Pathol. 2008 Mar;17(1):51-8. PMID: 18303406