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Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells

BACKGROUND: Archival formalin-fixed paraffin-embedded (FFPE) tissues have limited utility in applications involving analysis of gene expression due to mRNA degradation and modification during fixation and processing. This study analyzed 160 miRNAs in paired snap frozen and FFPE cells to investigate...

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Autores principales: Li, Jinghuan, Smyth, Paul, Flavin, Richard, Cahill, Susanne, Denning, Karen, Aherne, Sinead, Guenther, Simone M, O'Leary, John J, Sheils, Orla
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1914054/
https://www.ncbi.nlm.nih.gov/pubmed/17603869
http://dx.doi.org/10.1186/1472-6750-7-36
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author Li, Jinghuan
Smyth, Paul
Flavin, Richard
Cahill, Susanne
Denning, Karen
Aherne, Sinead
Guenther, Simone M
O'Leary, John J
Sheils, Orla
author_facet Li, Jinghuan
Smyth, Paul
Flavin, Richard
Cahill, Susanne
Denning, Karen
Aherne, Sinead
Guenther, Simone M
O'Leary, John J
Sheils, Orla
author_sort Li, Jinghuan
collection PubMed
description BACKGROUND: Archival formalin-fixed paraffin-embedded (FFPE) tissues have limited utility in applications involving analysis of gene expression due to mRNA degradation and modification during fixation and processing. This study analyzed 160 miRNAs in paired snap frozen and FFPE cells to investigate if miRNAs may be successfully detected in archival specimens. RESULTS: Our results show that miRNA extracted from FFPE blocks was successfully amplified using Q-RT-PCR. The levels of expression of miRNA detected in total RNA extracted from FFPE were higher than that extracted from snap frozen cells when the quantity of total RNA was identical. This phenomenon is most likely explained by the fact that larger numbers of FFPE cells were required to generate equivalent quantities of total RNA than their snap frozen counterparts. CONCLUSION: We hypothesise that methylol cross-links between RNA and protein which occur during tissue processing inhibit the yield of total RNA. However, small RNA molecules appear to be less affected by this process and are recovered more easily in the extraction process. In general miRNAs demonstrated reliable expression levels in FFPE compared with snap frozen paired samples, suggesting these molecules might prove to be robust targets amenable to detection in archival material in the molecular pathology setting.
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spelling pubmed-19140542007-07-13 Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells Li, Jinghuan Smyth, Paul Flavin, Richard Cahill, Susanne Denning, Karen Aherne, Sinead Guenther, Simone M O'Leary, John J Sheils, Orla BMC Biotechnol Research Article BACKGROUND: Archival formalin-fixed paraffin-embedded (FFPE) tissues have limited utility in applications involving analysis of gene expression due to mRNA degradation and modification during fixation and processing. This study analyzed 160 miRNAs in paired snap frozen and FFPE cells to investigate if miRNAs may be successfully detected in archival specimens. RESULTS: Our results show that miRNA extracted from FFPE blocks was successfully amplified using Q-RT-PCR. The levels of expression of miRNA detected in total RNA extracted from FFPE were higher than that extracted from snap frozen cells when the quantity of total RNA was identical. This phenomenon is most likely explained by the fact that larger numbers of FFPE cells were required to generate equivalent quantities of total RNA than their snap frozen counterparts. CONCLUSION: We hypothesise that methylol cross-links between RNA and protein which occur during tissue processing inhibit the yield of total RNA. However, small RNA molecules appear to be less affected by this process and are recovered more easily in the extraction process. In general miRNAs demonstrated reliable expression levels in FFPE compared with snap frozen paired samples, suggesting these molecules might prove to be robust targets amenable to detection in archival material in the molecular pathology setting. BioMed Central 2007-06-29 /pmc/articles/PMC1914054/ /pubmed/17603869 http://dx.doi.org/10.1186/1472-6750-7-36 Text en Copyright © 2007 Li et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Li, Jinghuan
Smyth, Paul
Flavin, Richard
Cahill, Susanne
Denning, Karen
Aherne, Sinead
Guenther, Simone M
O'Leary, John J
Sheils, Orla
Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells
title Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells
title_full Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells
title_fullStr Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells
title_full_unstemmed Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells
title_short Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells
title_sort comparison of mirna expression patterns using total rna extracted from matched samples of formalin-fixed paraffin-embedded (ffpe) cells and snap frozen cells
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1914054/
https://www.ncbi.nlm.nih.gov/pubmed/17603869
http://dx.doi.org/10.1186/1472-6750-7-36
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