Abstract
Retinoids and rexinoids directly and selectively activate their nuclear receptors, resulting in changes in the transcript levels of their target genes. Consequently, quantitating mRNA levels transcribed from cognate target genes is the most accurate measure of retinoid action. These changes can serve as relevant endpoints in biomarker trials, as well as in vivo preclinical studies. In gene expression analyses of archival material such as formalin-fixed paraffin-embedded (FFPE) tissues, assessing the quality of the extracted RNA is essential for the validation of the studies. With next generation sequencing (NGS) becoming the method of choice for gene expression profiling, RNA quality has become a critical aspect of study feasibility. In this chapter, we describe a method to extract RNA and to assess the intactness of RNA samples extracted from paraffin-embedded tissues.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Mazumdar A, Medina D, Kittrell FS, Zhang Y, Hill JL, Edwards DE, Bissonnette RP, Brown PH (2012) The combination of tamoxifen and the rexinoid LG100268 prevents ER-positive and ER-negative mammary tumors in p53-null mammary gland mice. Cancer Prev Res (Phila) 5(10):1195–1202. https://doi.org/10.1158/1940-6207.CAPR-11-0524
Garattini E, Bolis M, Garattini SK, Fratelli M, Centritto F, Paroni G, Gianni M, Zanetti A, Pagani A, Fisher JN, Zambelli A, Terao M (2014) Retinoids and breast cancer: from basic studies to the clinic and back again. Cancer Treat Rev 40(6):739–749. https://doi.org/10.1016/j.ctrv.2014.01.001
Uray IP, Connelly JH, Thomazy V, Shipley GL, Vaughn WK, Frazier OH, Taegtmeyer H, Davies PJ (2002) Left ventricular unloading alters receptor tyrosine kinase expression in the failing human heart. J Heart Lung Transplant 21(7):771–782
Ribeiro-Silva A, Zhang H, Jeffrey SS (2007) RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies. BMC Mol Biol 8:118. https://doi.org/10.1186/1471-2199-8-118
Shen Y, Li R, Tian F, Chen Z, Lu N, Bai Y, Ge Q, Lu Z (2018) Impact of RNA integrity and blood sample storage conditions on the gene expression analysis. Onco Targets Ther 11:3573–3581. https://doi.org/10.2147/OTT.S158868
Haynes HR, Killick-Cole CL, Hares KM, Redondo J, Kemp KC, Moutasim KA, Faulkner C, Wilkins A, Kurian KM (2018) Evaluation of the quality of RNA extracted from archival FFPE glioblastoma and epilepsy surgical samples for gene expression assays. J Clin Pathol 71(8):695–701. https://doi.org/10.1136/jclinpath-2017-204969
Jackson AF, Williams A, Moffat I, Phillips SL, Recio L, Waters MD, Lambert IB, Yauk CL (2013) Preparation of archival formalin-fixed paraffin-embedded mouse liver samples for use with the Agilent gene expression microarray platform. J Pharmacol Toxicol Methods 68(2):260–268. https://doi.org/10.1016/j.vascn.2013.02.008
Jaksik R, Iwanaszko M, Rzeszowska-Wolny J, Kimmel M (2015) Microarray experiments and factors which affect their reliability. Biol Direct 10:46. https://doi.org/10.1186/s13062-015-0077-2
de Kok JB, Roelofs RW, Giesendorf BA, Pennings JL, Waas ET, Feuth T, Swinkels DW, Span PN (2005) Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Lab Investig 85(1):154–159. https://doi.org/10.1038/labinvest.3700208
Zhuang Y, Faria TN, Chambon P, Gudas LJ (2003) Identification and characterization of retinoic acid receptor beta2 target genes in F9 teratocarcinoma cells. Mol Cancer Res 1(8):619–630
Uray IP, Dmitrovsky E, Brown PH (2016) Retinoids and rexinoids in cancer prevention: from laboratory to clinic. Semin Oncol 43(1):49–64. https://doi.org/10.1053/j.seminoncol.2015.09.002
Rajalingam D, Loftis C, Xu JJ, Kumar TK (2009) Trichloroacetic acid-induced protein precipitation involves the reversible association of a stable partially structured intermediate. Protein Sci 18(5):980–993. https://doi.org/10.1002/pro.108
Maniatis T (1982) Isolation and quantification of DNA1. In: Protocol 13 molecular cloning a laboratory manual, vol 1. Cold Spring Harbor Laboratory Press, New York, p 74
Chomczynski P (1992) Solubilization in formamide protects RNA from degradation. Nucleic Acids Res 20(14):3791–3792
Sarkar G, Kapelner S, Sommer SS (1990) Formamide can dramatically improve the specificity of PCR. Nucleic Acids Res 18(24):7465
Acknowledgments
This study was supported by the European Union and the European Regional Development Fund (GINOP-2.3.2-15-2016-00020). The publication was also supported by the “Debrecen Venture Catapult Program” (EFOP-3.6.1-16-2016-00022). The authors thank Dr. Karen Uray for critical reading of the manuscript.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Uray, I.P., László, L. (2019). Translation of Effects of Retinoids and Rexinoids: Extraction and Quality Assessment of RNA from Formalin-Fixed Tissues. In: Ray, S. (eds) Retinoid and Rexinoid Signaling . Methods in Molecular Biology, vol 2019. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9585-1_16
Download citation
DOI: https://doi.org/10.1007/978-1-4939-9585-1_16
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-4939-9584-4
Online ISBN: 978-1-4939-9585-1
eBook Packages: Springer Protocols