Effects of Cold Ischemia on Gene Expression: A Review and Commentary

Abstract

Frequently investigators request that tissues be collected and processed in less than one hour following removal from a patient. Some biorepositories expend significant personnel time and other resources in trying to meet such goals; however, it is unclear whether the perceived benefits of relatively short cold ischemia times warrant these added costs. The literature of human surgical tissues prospectively exposed to cold ischemia at several time points was reviewed to compare the changes in transcripts/genes and microRNA with time of cold ischemia. Also, reports of protein changes in response to cold ischemia were correlated to changes in genes. The literature is limited; however, for most tissues, only a small proportion of transcripts/genes (<1%) changes up to 3 hours following surgery and most transcripts increase rather than decrease in less than 2 hours of cold ischemia. Biorepositories and investigators must consider the literature for evidence of significant changes in molecular results from tissues before spending significant resources on relatively rapid collection of tissues to meet cold ischemia times of less than 3 hours. Instead, those using human tissues in research must consider if the cold ischemia times affect their use in specific research; hence are these tissues ''fit for purpose?''

Cold Ischemia Score: An mRNA Assay for the Detection of Extended Cold Ischemia in Formalin-Fixed, Paraffin-Embedded Tissue

“…This observation reflects the heterogeneity of biospecimens in general and has been made by others. 4,5 However, we found cold ischemia to be a larger driver of variability than either the sample collection site or the tissue type, and consequently, we think it must be considered a preanalytical variable of significance.…”

Factors that drive the increasing use of FFPE tissue in basic and translational cancer research

“…(Shi et al 2011). Not all results from translational research laboratories can be "readily reproduced," however, because tissue preparation methods are too variable or because of the involvement of other factors such as poor quality assurance or sample selection bias (Yeo et al 2014, Neumeister et al 2014, Atherton et al 2016.…”

“…Biological studies associated with multi-site clinical projects and trials that seek to establish the role of new biomarkers and associated targeted therapies usually rely on retrieval of existing FFPE archival tissue samples, derived from multiple pathology departments (Sparano et al 2015). Formalin fixation and tissue processing (Otali et al 2009, Atherton et al 2016, however, are not uniform in all specimen types, particularly in older resection specimens or from institution to institution. Therefore, critical decisions for advances in patient treatment might be based on examination of FFPE sections that may not be comparable.…”

“…Quality management and awareness of limitations of FFPE are vitally important (Bourgon et al 2014, Grizzle et al 2015, de Abreu et al 2016). Rigorous quality management and FFPE tissue prepreparation, including optimized library preparation, are required for clinical application of NGS (de Abreu et al 2016, Bolognesi et al 2016) applied to FFPE DNA to detect reproducibly copy number variations and single nucleotide variations (Shao et al 2016).…”

Next-Generation Sequencing in Diagnostic Pathology

“…As a general rule, the highest quality of DNA and RNA is obtained from tissue which is frozen as quickly as possible. Short delays in freezing will not affect the DNA but there may be subtle changes in the RNA expression profile (a phenomenon known as cold ischaemia) [41]. The circulating free DNA obtained from plasma is usually of high quality but is frequently fragmented due to cleavage prior to release from cell nuclei into the circulation.…”