201. Overcoming the Challenges of High Quality RNA Extraction from Core Needle Biopsy
- Author
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Rohann J.M. Correa, Dorien Autaers, Jan Jonckheere, Louise Cras, Keith Kwan, Kris Thielemans, Hanne Locy, Marian Vanhoeij, Stefanie Brock, Stefaan Verhulst, Karine Breckpot, A. Schiettecatte, Wim Waelput, Laboratory of Molecullar and Cellular Therapy, Basic (bio-) Medical Sciences, Faculty of Medicine and Pharmacy, Medical Imaging, Radiology, Supporting clinical sciences, Experimental Pathology, Pathology, Pathology/molecular and cellular medicine, Public Health Sciences, Liver Cell Biology, Surgical clinical sciences, Surgery, and Vriendenkring VUB
- Subjects
0301 basic medicine ,Core needle ,Small RNA ,Breast Neoplasms ,Computational biology ,Microbiology ,Biochemistry ,fresh-frozen ,Article ,Specimen Handling ,03 medical and health sciences ,0302 clinical medicine ,Breast cancer ,breast cancer ,Gene expression ,Biopsy ,medicine ,Humans ,biopsy ,Molecular Biology ,Cancer ,medicine.diagnostic_test ,business.industry ,Gene Expression Profiling ,RNA ,Reproducibility of Results ,formalin-fixed paraffin-embedded ,medicine.disease ,Microarray Analysis ,QR1-502 ,Gene expression profiling ,030104 developmental biology ,030220 oncology & carcinogenesis ,gene expression ,RNA extraction ,Biopsy, Large-Core Needle ,business - Abstract
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 smallRNA 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., The use of gene expression profiling (GEP) in cancer management is rising, as GEP provides insight in molecular and cellular processes through evaluation of thousands of genes at once. 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 input of RNA at sufficient quantity and quality. This highlights the need for standard procedures to ensure best practices for RNA extraction from tumor biopsies, which are often small 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, to homogenize or to deparaffinize tissues, and the impact of tissue composition on RNA extraction were studied. Additionally, the RNAs compatibility with the nanoString nCounter® technology was studied. This technology platform enables GEP using RNA and target specific probes of 50 bases that can bind to 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 could be used for RNA extraction. Both resulting RNA end products are compatible to the nanoString nCounter® technology.
- Published
- 2021