Abstract 361: Illuminating the effects of tissue degradation to improve the management of tissues used in cancer research or clinical applications

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA The collection and preservation of tissues from surgery to the lab affects the quality and value of research and/or healthcare applications for cancer patients. To this end we are further defining best practices in the management of surgically resected tissues through the analysis of a systems biology model. In the first steps of this process we defined an experimental animal model to assess gene expression signatures of biological pathways related to preservation intervals. Athymic nude murine tissues (kidney, liver, brain, and PDX-models) were excised at baseline and immediately aliquots of tissue were incubated at varying intervals (t=0, 0.5, 1, 3, 6, 9 hours, temperature during intervals was maintained at 37°C). All tissues were preserved at -80C and total RNA was extracted from these tissues using a uniform RNA isolation kit (RNeasy Mini Kit from Qiagen, Inc.) by the same technician. The RNA Integrity Number (RIN) was obtained using the Agilent's BioAnalyzer 2100 and RNA concentration using the Nanodrop 8000. Subsequently, cDNA was synthesized using Thermo Scientific's RevertAid First Strand cDNA Synthesis Kit, and qPCR analysis of each tissue was performed using the Qiagen RT2 Profiler PCR Arrays including the Cell Death PathwayFinder (murine origin liver, kidney, brain) and Hypoxia Signaling Pathway (human origin PDX-model) arrays. Results show a variation of transcripts s that were upregulated (Bax, Bcl2, Fos, Egr1, Tnfrsf10b) or downregulated (Ctss, Hmox1, Epo, Snca) with increased length of tissue incubation and tissue-specific patterns of regulation were observed. Furthermore, these changes in gene expression did not correlate with a decrease in RIN scores, which raises questions about the suitability of RIN as a comprehensive assessment of RNA quality at the transcript level. These findings have important implications for cancer research, namely that tissues that have not been stabilized within several minutes of excision from the host might have undergone degradation of RNA templates that reflect tissue management-related biological activity versus disease-related transcriptome. In future work, we plan to compare macroanalytes such as microRNAs, non-coding RNAs and proteins across different tissue types with an assumption that gene signatures and biological effects will differ per tissue type. We will use results from our experimental biopreservation model to continue the emphasis on transcriptome changes within the context of biological relevance. Citation Format: Scott D. Jewell, Eric Collins, John Beck, David Monsma, Dawna Dylewski, Andrew Borgman, Mary Winn, Galen Hostetter. Illuminating the effects of tissue degradation to improve the management of tissues used in cancer research or clinical applications. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 361. doi:10.1158/1538-7445.AM2014-361