ArticlePloS one2013
Effects of warm ischemic time on gene expression profiling in colorectal cancer tissues and normal mucosa.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 27 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
27 citing papers in PubMed, 62 citations in OpenAlex.
- Pre-analytical Best Practices for RNA Sequencing from Small Biopsies and Cytologic Specimens.Molecular diagnosis & therapy · 2026Review
- Transcriptional activation of LINGO1 facilitates proliferation and immune escape in colorectal cancer.Scientific reports · 2026Article
- BAP1-mediated stabilization of SUFU enhances E2F1 activity and promotes colorectal tumorigenesis.Cell communication and signaling : CCS · 2026Article
- The effect of cold ischemia time on hypoxia, EMT, and apoptosis pathways in normal colon mucosa.PloS one · 2026Article
- Bayesian Multi-Group Gaussian Process Models for Heterogeneous Group-Structured Data.Journal of machine learning research : JMLR · 2025Article
- NXPH4 mediated by mCellular & molecular biology letters · 2024Article
- Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks.Briefings in bioinformatics · 2022Article
- Serum-based measurements of stromal activation through ADAM12 associate with poor prognosis in colorectal cancer.BMC cancer · 2022Article
- Downregulation of B3GNT6 is a predictor of poor outcomes in patients with colorectal cancer.World journal of surgical oncology · 2022Article
- Assessing the quality of RNA isolated from human breast tissue after ambient room temperature exposure.PloS one · 2022Article
- SELENBP1 inhibits progression of colorectal cancer by suppressing epithelial-mesenchymal transition.Open medicine (Warsaw, Poland) · 2022Article
- Employing bioinformatics analysis to identify hub genes and microRNAs involved in colorectal cancer.Medical oncology (Northwood, London, England) · 2021Article
- GABRD promotes progression and predicts poor prognosis in colorectal cancer.Open medicine (Warsaw, Poland) · 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
- Audit of Quality and Quantity of Nucleic Acid Yield from Pediatric Acute Leukemia Cases Following a Bio-banking Initiative.Indian journal of hematology & blood transfusion : an official journal of Indian Society of Hematology and Blood Transfusion · 2019Article
- The effects of death and post-mortem cold ischemia on human tissue transcriptomes.Nature communications · 2018Article
- Tumor Pre-Analytics in Molecular Pathology: Impact on Protein Expression and Analysis.Current pathobiology reports · 2018Review
- Effects of Cold Ischemia on Gene Expression: A Review and Commentary.Biopreservation and biobanking · 2016Review
- The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data.Scientific reports · 2016Article
- Biobanking of Fresh-Frozen Human Adenocarcinomatous and Normal Colon Tissues: Which Parameters Influence RNA Quality?PloS one · 2016Article
Corrections and comments
- Erratum issuedMassimo, Milione [corrected to Milione, Massimo]
Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome-wide gene expression analyses of tumors are a powerful tool to identify gene signatures associated with biologically and clinically relevant characteristics and for several tumor types are under clinical validation by prospective trials. However, handling and processing of clinical specimens may significantly affect the molecular data obtained from their analysis. We studied the effects of tissue handling time on gene expression in human normal and tumor colon tissues undergoing routine surgical procedures.
methodsRNA extracted from specimens of 15 patients at four time points (for a total of 180 samples) after surgery was analyzed for gene expression on high-density oligonucleotide microarrays. A mixed-effects model was used to identify probes with different expression means across the four different time points. The p-values of the model were adjusted with the Bonferroni method.
resultsThirty-two probe sets associated with tissue handling time in the tumor specimens, and thirty-one in the normal tissues, were identified. Most genes exhibited moderate changes in expression over the time points analyzed; however four of them were oncogenes, and two confirmed the effect of tissue handling by independent validation.
conclusionsOur results suggest that a critical time point for tissue handling in colon seems to be 60 minutes at room temperature. Although the number of time-dependent genes we identified was low, the three genes that already showed changes at this time point in tumor samples were all oncogenes, hence recommending standardization of tissue-handling protocols and effort to reduce the time from specimen removal to snap freezing accounting for warm ischemia in this tumor type.
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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.