Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.

The quality of tissue samples and extracted mRNA is a major source of variability in tumor transcriptome analysis using genome-wide expression microarrays. During and immediately after surgical tumor resection, tissues are exposed to metabolic, biochemical and physical stresses characterized as &quo...

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Autores principales:	Elodie Caboux, Maria Paciencia, Geoffroy Durand, Nivonirina Robinot, Magdalena B Wozniak, Françoise Galateau-Salle, Graham Byrnes, Pierre Hainaut, Florence Le Calvez-Kelm
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/18e496b5f0484fe89c3f3e7a112acbed
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spelling	oai:doaj.org-article:18e496b5f0484fe89c3f3e7a112acbed2021-11-18T08:45:31ZImpact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.1932-620310.1371/journal.pone.0079826https://doaj.org/article/18e496b5f0484fe89c3f3e7a112acbed2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24278187/?tool=EBIhttps://doaj.org/toc/1932-6203The quality of tissue samples and extracted mRNA is a major source of variability in tumor transcriptome analysis using genome-wide expression microarrays. During and immediately after surgical tumor resection, tissues are exposed to metabolic, biochemical and physical stresses characterized as "warm ischemia". Current practice advocates cryopreservation of biosamples within 30 minutes of resection, but this recommendation has not been systematically validated by measurements of mRNA decay over time. Using Illumina HumanHT-12 v3 Expression BeadChips, providing a genome-wide coverage of over 24,000 genes, we have analyzed gene expression variation in samples of 3 hepatocellular carcinomas (HCC) and 3 lung carcinomas (LC) cryopreserved at times up to 2 hours after resection. RNA Integrity Numbers (RIN) revealed no significant deterioration of mRNA up to 2 hours after resection. Genome-wide transcriptome analysis detected non-significant gene expression variations of -3.5%/hr (95% CI: -7.0%/hr to 0.1%/hr; p = 0.054). In LC, no consistent gene expression pattern was detected in relation with warm ischemia. In HCC, a signature of 6 up-regulated genes (CYP2E1, IGLL1, CABYR, CLDN2, NQO1, SCL13A5) and 6 down-regulated genes (MT1G, MT1H, MT1E, MT1F, HABP2, SPINK1) was identified (FDR <0.05). Overall, our observations support current recommendation of time to cryopreservation of up to 30 minutes and emphasize the need for identifying tissue-specific genes deregulated following resection to avoid misinterpreting expression changes induced by warm ischemia as pathologically significant changes.Elodie CabouxMaria PacienciaGeoffroy DurandNivonirina RobinotMagdalena B WozniakFrançoise Galateau-SalleGraham ByrnesPierre HainautFlorence Le Calvez-KelmPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 11, p e79826 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Elodie Caboux Maria Paciencia Geoffroy Durand Nivonirina Robinot Magdalena B Wozniak Françoise Galateau-Salle Graham Byrnes Pierre Hainaut Florence Le Calvez-Kelm Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.
description	The quality of tissue samples and extracted mRNA is a major source of variability in tumor transcriptome analysis using genome-wide expression microarrays. During and immediately after surgical tumor resection, tissues are exposed to metabolic, biochemical and physical stresses characterized as "warm ischemia". Current practice advocates cryopreservation of biosamples within 30 minutes of resection, but this recommendation has not been systematically validated by measurements of mRNA decay over time. Using Illumina HumanHT-12 v3 Expression BeadChips, providing a genome-wide coverage of over 24,000 genes, we have analyzed gene expression variation in samples of 3 hepatocellular carcinomas (HCC) and 3 lung carcinomas (LC) cryopreserved at times up to 2 hours after resection. RNA Integrity Numbers (RIN) revealed no significant deterioration of mRNA up to 2 hours after resection. Genome-wide transcriptome analysis detected non-significant gene expression variations of -3.5%/hr (95% CI: -7.0%/hr to 0.1%/hr; p = 0.054). In LC, no consistent gene expression pattern was detected in relation with warm ischemia. In HCC, a signature of 6 up-regulated genes (CYP2E1, IGLL1, CABYR, CLDN2, NQO1, SCL13A5) and 6 down-regulated genes (MT1G, MT1H, MT1E, MT1F, HABP2, SPINK1) was identified (FDR <0.05). Overall, our observations support current recommendation of time to cryopreservation of up to 30 minutes and emphasize the need for identifying tissue-specific genes deregulated following resection to avoid misinterpreting expression changes induced by warm ischemia as pathologically significant changes.
format	article
author	Elodie Caboux Maria Paciencia Geoffroy Durand Nivonirina Robinot Magdalena B Wozniak Françoise Galateau-Salle Graham Byrnes Pierre Hainaut Florence Le Calvez-Kelm
author_facet	Elodie Caboux Maria Paciencia Geoffroy Durand Nivonirina Robinot Magdalena B Wozniak Françoise Galateau-Salle Graham Byrnes Pierre Hainaut Florence Le Calvez-Kelm
author_sort	Elodie Caboux
title	Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.
title_short	Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.
title_full	Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.
title_fullStr	Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.
title_full_unstemmed	Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.
title_sort	impact of delay to cryopreservation on rna integrity and genome-wide expression profiles in resected tumor samples.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/18e496b5f0484fe89c3f3e7a112acbed
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Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.

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