RNA Quality in Fresh-Frozen Gastrointestinal Tumor Specimens—Experiences from the Tumor and Healthy Tissue Bank TU Dresden

Abstract

The term "pre-analytics" summarizes all procedures concerned with specimen collection or processing as well as logistical aspects like transport or storage of tissue specimens. All or these variables as well as tissue-specific characteristics affect sample quality. While certain parameters like warm ischemia or tissue-specific characteristics cannot be changed, other parameters can be assessed and optimized. The aim of this study was to determine RNA quality by assessing the RIN values of specimens from different organs and to assess the influence of vacuum preservation. Samples from the GI tract, in general, appear to have lower RNA quality when compared to samples from other organ sites. This may be due to the digestive enzymes or bacterial colonization. Processing time in pathology does not significantly influence RNA quality. Tissue preservation with a vacuum sealer leads to preserved RNA quality over an extended period of time and offers a feasible alternative to minimize the influence of transport time into pathology.

Factors That Influence the Quality of RNA From the Pancreas of Organ Donors

“…8 Zeugner et al showed that vacuum-sealing of tissue for short-term storage prior to RNA extraction can minimize the drop in RNA quality. 6 The Genotype-Tissue Expression (GTEx) Consortium reported that RNA quality dropped in samples with longer ischemia times, 2 a finding contrary to Taurianinen 7 and Rudloff 8 ; however, sample types and preservation methods differed between studies.…”

“…2 This is particularly true of the pancreas, where elevated levels of ribonuclease1 (RNAse1), a double-stranded RNA-degrading enzyme, are present. 3–5 For example, when compared to a panel of tissues taken from different donors 6 or the same individual, 2 RNA quality of most pancreas samples were found to be lower than ½ to ¾ of all tissue types tested, respectively.…”

“…2,6–8 Tauriainen et al found that the storage of pancreas tissue up to 6 years in RNA later , a medium that inhibits RNAse activity, preserved the quality of RNA once extracted. 7 Likewise, Rudloff et al did not find any quality differences in RNA extracted from samples stored for different time periods in Optimal Cutting Temperature (OCT) compound, a medium that is used for tissue embedding prior to sample sectioning.…”

“…Most of the available research is based on samples obtained from surgical biopsy, 6,12,18 autopsy donations, 9–11,13,15,16 or the placenta 14,17 ; very few studies include the use of pancreata from human organ donations. 2,7 This is important because the logistics and timing of organ or tissue recovery are very different depending on the source of the samples.…”

“…Moreover, many studies used only tumor 6,8 or diseased 11,12,16 tissue, did not access RNA quality in a comparable manner, 7,10,15 nor were measures of outcome statistically quantified. 2,6,7,10 The importance of these previously established, and newly proposed, variables in maximizing human pancreas RNA quality have not been evaluated alone or in combination with one another. Therefore, this study was performed to identify predictors that increase the odds of obtaining high quality human pancreatic RNA in samples made available through the Network for Pancreatic Organ Donors with Diabetes (nPOD) program.…”