Effects of ex vivo ischemia time and delayed processing on quality of specimens in tissue biobank

Guo,Dan; Wang,Anqi; Xie,Ting; Zhang,Sumei; Cao,Dingyan; Sun,Jian

doi:10.3892/mmr.2020.11503

Effects of ex vivo ischemia time and delayed processing on quality of specimens in tissue biobank

Authors:
- Dan Guo
- Anqi Wang
- Ting Xie
- Sumei Zhang
- Dingyan Cao
- Jian Sun
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Affiliations: Clinical Biobank, Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
Published online on: September 10, 2020 https://doi.org/10.3892/mmr.2020.11503
Pages: 4278-4288
Copyright: © Guo et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

The RNA quality of tissue biobank is crucial for translational research; however, the effects of the ex vivo ischemia time on RNA integrity and expression of genes related to hypoxia, stress, apoptosis and autophagy remains elusive. A total of 18 carcinoma tissues were stored at room temperature for 15 min, 30 min, 1, 2, 4, 8 and 24 h. The integrity and purity of isolated RNA were analyzed. Furthermore, the gene expression of mTOR, hypoxia‑inducible factor 1α, phosphatidylinositol 4,5‑bisphosphate 3‑kinase catalytic subunit β isoform (PI3KCB), threonine kinase 1 (AKT1), NF‑κB, protein kinase AMP‑activated catalytic subunit α1 (AMPKα1), caspase 8 (CASP8), unc‑51 like autophagy activating kinase 1 and Fas cell surface death receptor were analyzed using reverse transcription‑quantitative PCR. The results demonstrated that RNA integrity numbers (RINs) remained stable in carcinoma tissues following ex vivo ischemia for 2 h at room temperature and that degradation began at 4 h (P<0.001). Additionally, the expression of PI3KCB, AKT1, AMPKα1 and CASP8 decreased at time points 8‑24 h following ex vivo ischemia and delayed processing (P<0.001). In conclusion, >2 h of ex vivo ischemia and delayed processing induced RNA degradation and RIN, and the gene expressions of PI3KCB, AKT, AMPKα1 and CASP8 may be considered as markers to evaluate tissue quality at the gene expression level, providing a method for the standard processing and assessment of tissue specimen.

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1	Watson PH, Wilson-McManus JE, Barnes RO, Barnes, Giesz SC, Png A, Hegele RG, Brinkman JN, Mackenzie IR, Huntsman DG, Junker A, et al: Evolutionary concepts in biobanking-the BC BioLibrary. J Transl Med. 7:952009. View Article : Google Scholar : PubMed/NCBI
2	Nishihara H: Clinical biobank: A novel system to support cancer clinical sequencing in Japan. Rinsho Byori. 65:167–172. 2017.(In Japanese). PubMed/NCBI
3	Ginsburg GS, Burke TW and Febbo P: Centralized biorepositories for genetic and genomic research. JAMA. 299:1359–1361. 2008. View Article : Google Scholar : PubMed/NCBI
4	Baker M: Biorepositories: Building better biobanks. Nature. 486:141–146. 2012. View Article : Google Scholar : PubMed/NCBI
5	Carithers LJ, Agarwal R, Guan P, Odeh H, Sachs MC, Engel KB, Greytak SR, Barcus M, Soria C, Jason Lih CJ, et al: The biospecimen preanalytical variables program: A multiassay comparison of effects of delay to fixation and fixation duration on nucleic acid quality. Arch Pathol Lab Med. 143:1106–1118. 2019. View Article : Google Scholar : PubMed/NCBI
6	Compton CC, Robb JA, Anderson MW, Berry AB, Birdsong GG, Bloom KJ, Branton PA, Crothers JW, Cushman-Vokoun AM, Hicks DG, et al: Preanalytics and precision pathology: Pathology practices to ensure molecular integrity of cancer patient biospecimens for precision medicine. Arch Pathol Lab Med. 143:1346–1363. 2019. View Article : Google Scholar : PubMed/NCBI
7	Kahn N, Riedlinger J, Roessler M, Rabe C, Lindner M, Koch I, Schott-Hildebrand S, Herth FJ, Schneider MA, Meister M and Muley TR: Blood-sampling collection prior to surgery may have a significant influence upon biomarker concentrations measured. Clin Proteomics. 12:192015. View Article : Google Scholar : PubMed/NCBI
8	Galissier T, Schneider C, Nasri S, Kanagaratnam L, Fichel C, Coquelet C, Diebold MD, Kianmanesh R, Bellon G, Dedieu S, et al: Biobanking of fresh-frozen human adenocarcinomatous and normal colon tissues: Which parameters influence RNA quality? PLoS One. 11:e01543262016. View Article : Google Scholar : PubMed/NCBI
9	Zhou JH, Sahin AA and Myers JN: Biobanking in genomic medicine. Arch Pathol Lab Med. 139:812–818. 2015. View Article : Google Scholar : PubMed/NCBI
10	Olsen J, Kirkeby LT, Eiholm S, Jess P, Troelsen JT, Gögenür I and Olsen J: Impact of in vivo ischemic time on RNA quality-experiences from a colon cancer biobank. Biopreserv Biobank. 13:255–262. 2015. View Article : Google Scholar : PubMed/NCBI
11	Zheng XH, Zhang SD, Zhang PF, Li XZ, Hu YZ, Tian T, Zhu L, Wang RZ and Jia WH: Tumor cell content and RNA integrity of surgical tissues from different types of tumors and its correlation with ex vivo and in vivo ischemia. Ann Surg Oncol. 25:3764–3770. 2018. View Article : Google Scholar : PubMed/NCBI
12	Betsou F, Lehmann S, Ashton G, Barnes M, Benson EE, Coppola D, DeSouza Y, Eliason J, Glazer B, Guadagni F, et al: Standard preanalytical coding for biospecimens: Defining the sample PREanalytical code. Cancer Epidemiol Biomarkers Prev. 19:1004–1011. 2010. View Article : Google Scholar : PubMed/NCBI
13	Mazzei M, Vascellari M, Zanardello C, Melchiotti E, Vannini S, Forzan M, Marchetti V, Albanese F and Abramo F: Quantitative real time polymerase chain reaction (qRT-PCR) and RNAscope in situ hybridization (RNA-ISH) as effective tools to diagnose feline herpesvirus-1-associated dermatitis. Vet Dermatol. 30:491–e147. 2019. View Article : Google Scholar : PubMed/NCBI
14	Livak KJ and Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods. 25:402–408. 2001. View Article : Google Scholar : PubMed/NCBI
15	Micke P, Ohshima M, Tahmasebpoor S, Ren ZP, Ostman A, Pontén F and Botling J: Biobanking of fresh frozen tissue: RNA is stable in nonfixed surgical specimens. Lab Invest. 86:202–211. 2006. View Article : Google Scholar : PubMed/NCBI
16	Rudloff U, Bhanot U, Gerald W, Klimstra DS, Jarnagin WR, Brennan MF and Allen PJ: Biobanking of human pancreas cancer tissue: Impact of ex-vivo procurement times on RNA quality. Ann Surg Oncol. 17:2229–2236. 2010. View Article : Google Scholar : PubMed/NCBI
17	Bao WG, Zhang X, Zhang JG, Zhou WJ, Bi TN, Wang JC, Yan WH and Lin A: Biobanking of fresh-frozen human colon tissues: Impact of tissue ex-vivo ischemia times and storage periods on RNA quality. Ann Surg Oncol. 20:1737–1744. 2013. View Article : Google Scholar : PubMed/NCBI
18	Lee SM, Schelcher C, Thasler R, Schiergens TS and Thasler WE: Pre-analytical determination of the effect of extended warm or cold ischaemia on RNA stability in the human ileum mucosa. PLoS One. 10:e01382142015. View Article : Google Scholar : PubMed/NCBI
19	Jeck WR, Sorrentino JA, Wang K, Slevin MK, Burd CE, Liu J, Marzluff WF and Sharpless NE: Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA. 19:141–157. 2013. View Article : Google Scholar : PubMed/NCBI
20	Sun H, Sun R, Hao M, Wang Y, Zhang X, Liu Y and Cong X: Effect of duration of ex vivo ischemia time and storage period on RNA quality in biobanked human renal cell carcinoma tissue. Ann Surg Oncol. 23:297–304. 2016. View Article : Google Scholar : PubMed/NCBI
21	Zheng H, Tao YP, Chen FQ, Li HF, Zhang ZD, Zhou XX, Yang Y and Zhou WP: Temporary ischemia time before snap freezing is important for maintaining high-integrity RNA in hepatocellular carcinoma tissues. Biopreserv Biobank. 17:425–432. 2019. View Article : Google Scholar : PubMed/NCBI
22	Guerrera F, Tabbo F, Bessone L, Maletta F, Gaudiano M, Ercole E, Annaratone L, Todaro M, Boita M, Filosso PL, et al: The influence of tissue ischemia time on RNA integrity and patient-derived xenografts (PDX) engraftment rate in a non-small cell lung cancer (NSCLC) biobank. PLoS One. 11:e01451002016. View Article : Google Scholar : PubMed/NCBI
23	Castells Domingo X, Ferrer-Font L, Davila M, Candiota AP, Simões RV, Fernández-Coello A, Gabarrós A, Boluda S, Barceló A, Ariño J and Arús C: Improving ribosomal RNA integrity in surgically resected human brain tumor biopsies. Biopreserv Biobank. 14:156–164. 2016. View Article : Google Scholar : PubMed/NCBI
24	Gonzalez-Herrera L, Valenzuela A, Marchal JA, Lorente JA and Villanueva E: Studies on RNA integrity and gene expression in human myocardial tissue, pericardial fluid and blood, and its postmortem stability. Forensic Sci Int. 232:218–228. 2013. View Article : Google Scholar : PubMed/NCBI
25	Song SY, Jun J, Park M, Park SK, Choi W, Park K, Jang KT and Lee M: Biobanking of fresh-frozen cancer tissue: RNA is stable independent of tissue type with less than 1 hour of cold ischemia. Biopreserv Biobank. 16:28–35. 2018. View Article : Google Scholar : PubMed/NCBI
26	Wang Z, Wang Y, Ye J, Lu X, Cheng Y, Xiang L, Chen L, Feng W, Shi H, Yu X, et al: bFGF attenuates endoplasmic reticulum stress and mitochondrial injury on myocardial ischaemia/reperfusion via activation of PI3K/Akt/ERK1/2 pathway. J Cell Mol Med. 19:595–607. 2015. View Article : Google Scholar : PubMed/NCBI
27	Chen CM, Wu CT, Yang TH, Chang YA, Sheu ML and Liu SH: Green tea catechin prevents hypoxia/reperfusion-evoked oxidative stress-regulated autophagy-activated apoptosis and cell death in microglial cells. J Agric Food Chem. 64:4078–4085. 2016. View Article : Google Scholar : PubMed/NCBI
28	Mihaylova MM and Shaw RJ: The AMPK signalling pathway coordinates cell growth, autophagy and metabolism. Nat Cell Biol. 13:1016–1023. 2011. View Article : Google Scholar : PubMed/NCBI
29	Qi D and Young LH: AMPK: Energy sensor and survival mechanism in the ischemic heart. Trends Endocrinol Metab. 26:422–429. 2015. View Article : Google Scholar : PubMed/NCBI
30	Hers I, Vincent EE and Tavare JM: Akt signalling in health and disease. Cell Signal. 23:1515–1527. 2011. View Article : Google Scholar : PubMed/NCBI
31	Manning BD and Cantley LC: AKT/PKB signaling: Navigating downstream. Cell. 129:1261–1274. 2007. View Article : Google Scholar : PubMed/NCBI
32	Avalos Y, Canales J, Bravo-Sagua R, Criollo A, Lavandero S and Quest AF: Tumor suppression and promotion by autophagy. Biomed Res Int. 2014:6039802014. View Article : Google Scholar : PubMed/NCBI
33	Iurlaro R and Munoz-Pinedo C: Cell death induced by endoplasmic reticulum stress. FEBS J. 283:2640–2652. 2016. View Article : Google Scholar : PubMed/NCBI
34	Saggioro FP, Neder L, Stavale JN, Paixão-Becker ANP, Malheiros SMF, Soares FA, Pittella JEH, Matias CCMS, Colli BO, Carlotti CG Jr and Franco M: Fas, FasL, and cleaved caspases 8 and 3 in glioblastomas: A tissue microarray-based study. Pathol Res Pract. 210:267–273. 2014. View Article : Google Scholar : PubMed/NCBI
35	Schito L and Semenza GL: Hypoxia-inducible factors: Master regulators of cancer progression. Trends Cancer. 2:758–770. 2016. View Article : Google Scholar : PubMed/NCBI
36	LaGory EL and Giaccia AJ: The ever-expanding role of HIF in tumour and stromal biology. Nat Cell Biol. 18:356–365. 2016. View Article : Google Scholar : PubMed/NCBI
37	Kurokawa M and Kornbluth S: Caspases and kinases in a death grip. Cell. 138:838–854. 2009. View Article : Google Scholar : PubMed/NCBI
38	Lange N, Unger FT, Schoppler M, Pursche K, Juhl H and David KA: Identification and validation of a potential marker of tissue quality using gene expression analysis of human colorectal tissue. PLoS One. 10:e01339872015. View Article : Google Scholar : PubMed/NCBI
39	Pietrocola F, Izzo V, Niso-Santano M, Vacchelli E, Galluzzi L, Maiuri MC and Kroemer G: Regulation of autophagy by stress-responsive transcription factors. Semin Cancer Biol. 23:310–322. 2013. View Article : Google Scholar : PubMed/NCBI
40	Verzella D, Pescatore A, Capece D, Vecchiotti D, Ursini MV, Franzoso G, Alesse E and Zazzeroni F: Life, death, and autophagy in cancer: NF-κB turns up everywhere. Cell Death Dis. 11:2102020. View Article : Google Scholar : PubMed/NCBI
41	Karar J and Maity A: PI3K/AKT/mTOR pathway in angiogenesis. Front Mol Neurosci. 4:512011. View Article : Google Scholar : PubMed/NCBI
42	Nazarko VY and Zhong Q: ULK1 targets beclin-1 in autophagy. Nat Cell Biol. 15:727–728. 2013. View Article : Google Scholar : PubMed/NCBI
43	Kim SJ, Dix DJ, Thompson KE, Murrell RN, Schmid JE, Gallagher JE and Rockett JC: Effects of storage, RNA extraction, genechip type, and donor sex on gene expression profiling of human whole blood. Clin Chem. 53:1038–1045. 2007. View Article : Google Scholar : PubMed/NCBI
44	Becker N and Lockwood CM: Pre-analytical variables in miRNA analysis. Clin Biochem. 46:861–868. 2013. View Article : Google Scholar : PubMed/NCBI
45	Willemse EA and Teunissen CE: Biobanking of cerebrospinal fluid for biomarker analysis in neurological diseases. Adv Exp Med Biol. 864:79–93. 2015. View Article : Google Scholar : PubMed/NCBI