Ischemia caused by time to freezing induces systematic microRNA and mRNA responses in cancer tissue

Time to freezing tumor tissue for RNA expression analysis will always vary to some extent. To evaluate the effect of ischemia time, tumor tissue from ten breast cancer patients was collected and aliquots of tissue were snap frozen at different time points after surgery (0, 0.5, 1, 3 and 6 h). Using miRNA and mRNA expression microarrays and statistical analysis, 56 miRNAs and 1788 mRNAs were found to be significantly altered with ischemia time up to six hours. Several of the 56 miRNAs have been reported to play a role in cancer, such as hsa-miR-663 and hsa-miR-125a-3p. Known stress response genes such as GADD45B, JUND and FOSB were among the mRNAs most significantly affected by time to freezing. A novel statistical method for identification of consistently correlated miRNA–mRNA pairs and miRNA-associated biological processes in time course data is presented. Application of this method revealed that several miRNAs, including hsa-miR-1228, hsa-miR-1225-5p and hsa-miR-574-5p, were associated through their correlation to mRNAs to biological processes such as “response to stimulus” and “stress response”. These miRNAs also showed enrichment of predicted targets among either their positively or negatively correlated mRNAs. The induced miRNAs may play both direct and indirect roles in biological responses. Caution should be taken when the miRNAs and mRNAs reported to be affected by ischemia time are included in a prognostic or predictive signature.

► Breast cancer tissue was snap frozen at different time points after surgery.
► The expression levels of 56 miRNAs and 1788 mRNAs were altered with ischemia time.
► The top miRNAs and mRNAs increased in expression levels with time.
► Several miRNAs were associated to “response to stimulus” and “stress response”.
► A novel statistical method for analyzing time course data is presented.