ArticlePloS one2013
Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 23 citations in OpenAlex.
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- Single-Cell Sequencing and Its Applications in Liver Cancer.Frontiers in oncology · 2022Review
- Addressing the quality challenge of a human biospecimen biobank through the creation of a quality management system.PloS one · 2022Article
- Optimization of RNA extraction methods from human metabolic tissue samples of the COMET biobank.Scientific reports · 2021Article
- Article
- Characterising cellular and molecular features of human peripheral nerve degeneration.Acta neuropathologica communications · 2020Article
- Cryopreservation Induces Alterations of miRNA and mRNA Fragment Profiles of Bull Sperm.Frontiers in genetics · 2020Article
- Biobanking and cryopreservation of human lung explants for omic analysis.The European respiratory journal · 2020Article
- In search of an evidence-based strategy for quality assessment of human tissue samples: report of the tissue Biospecimen Research Working Group of the Spanish Biobank Network.Journal of translational medicine · 2019Review
- The Effects of Surgical Antiseptics and Time Delays on RNA Isolated From Human and Rodent Peripheral Nerves.Frontiers in cellular neuroscience · 2019Article
- Successful Secondary Engraftment of Pancreatic Ductal Adenocarcinoma and Cholangiocarcinoma Patient-Derived Xenografts After Previous Failed Primary Engraftment.Translational oncology · 2019Article
- Recommendations for improving accuracy of gene expression data in bone and cartilage tissue engineering.Scientific reports · 2018Article
- Nanoproteomic analysis of ischemia-dependent changes in signaling protein phosphorylation in colorectal normal and cancer tissue.Journal of translational medicine · 2016Article
- The effect of freezing on the immunoprofile of breast carcinoma cells.Balkan medical journal · 2014Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.