Overcoming the Challenges of High Quality RNA Extraction from Core Needle Biopsy

Biomolecules

Stefanie Brock¹  Wim Waelput¹  Louise Cras¹  Keith Kwan²  RohannJ.M. Correa³  Ann Schiettecatte⁴  Jan Jonckheere⁴  Marian Vanhoeij⁵  Kris Thielemans⁶  Hanne Locy⁶  Karine Breckpot⁶  Dorien Autaers⁶  Stefaan Verhulst⁷ 

[1] Department of Anatomo-Pathology, UZ Brussel, Laarbeeklaan 101, B-1090 Brussels, Belgium;Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;Department of Radiation Oncology, London Regional Cancer Program, London Health Sciences Centre, 800 Commisioners Road East, London, ON N6A 4G5, Canada;Department of Radiology, Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B-1090 Brussels, Belgium;Department of Surgery, UZ Brussel, Laarbeeklaan 101, B-1090 Brussels, Belgium;Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103/E, B-1090 Brussels, Belgium;Liver Cell Biology Research Group, Department of Biomedical Sciences, VUB, Laarbeeklaan 103/D, B-1090 Brussels, Belgium;

关键词: breast cancer;    fresh-frozen;    formalin-fixed paraffin-embedded;    biopsy;    RNA;    gene expression;   

DOI  :  10.3390/biom11050621

来源: DOAJ

【 摘 要 】

The use of gene expression profiling (GEP) in cancer management is rising, as GEP can be used for disease classification and diagnosis, tailoring treatment to underlying genetic determinants of pharmacological response, monitoring of therapy response, and prognosis. However, the reliability of GEP heavily depends on the input of RNA in sufficient quantity and quality. This highlights the need for standard procedures to ensure best practices for RNA extraction from often small tumor biopsies with variable tissue handling. We optimized an RNA extraction protocol from fresh-frozen (FF) core needle biopsies (CNB) from breast cancer patients and from formalin-fixed paraffin-embedded (FFPE) tissue when FF CNB did not yield sufficient RNA. Methods to avoid ribonucleases andto homogenize or to deparaffinize tissues and the impact of tissue composition on RNA extraction were studied. Additionally, RNA’s compatibility with the nanoString nCounter^® technology was studied. This technology platform enables GEP using small RNA fragments. After optimization of the protocol, RNA of high quality and sufficient quantity was obtained from FF CNB in 92% of samples. For the remaining 8% of cases, FFPE material prepared by the pathology department was used for RNA extraction. Both resulting RNA end products are compatible with the nanoString nCounter^® technology.

【 授权许可】

Unknown