Fit for Purpose Frozen Tissue Collections by RNA Integrity Number-Based Quality Control Assurance at the Erasmus MC Tissue Bank

Kap, Marcel; Oomen, M.H.A.; Arshad, Shazia; Jong, Bas de; Riegman, Peter

doi:10.1089/bio.2013.0051

Cited by 42 publications

(44 citation statements)

References 16 publications

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“…The majority of studies investigated the association between RNA quality, as measured by RIN and/or 28S/18S, and storage time17 18 21–23 25–30 and/or temperature 12 17–27 29 30. The findings overwhelmingly indicated that RNA quality and integrity were not affected by either measure, and that RNA was highly stable for several hours,12 17–19 22 25–28 30 including overnight at room temperature 12.…”

Section: Resultsmentioning

confidence: 99%

Quality assessment and preservation of RNA from biobank tissue specimens: a systematic review

2015

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It is well recognised that genomic, proteomic and biomarker studies require properly annotated and well-characterised biospecimens. Consequently, this necessitates biobanks to collect, store and distribute biospecimens under stringent quality control and assurance measures. However, despite this realisation, there remains a lack of standardisation in quality management among biobanks and consensus as to which quality indicators provide the optimal molecular diagnostic performance tools and information for biospecimens. In an attempt to identify key factors that predict tissue specimen integrity and quality, this systematic review investigated the measures reported in the literature, which characterised the collection, processing and storage of high-quality tissue specimens. Our findings demonstrated RNA integrity, alone, may not be an effective measure of tissue quality. Furthermore, the frequently reported parameters related to biospecimen integrity, such as storage time, temperature, time to cryopreservation and tissue morphology were also not effective indicators of quality control and assurance. These findings suggest that it is unlikely that a single marker will provide the optimal diagnostic and performance information for biospecimens, but rather, a panel of markers assessing the molecular integrity of the lifespan of the biospecimen is required. Further work is needed to identify which factors predict specimen integrity and quality in biobanked tissue specimens.

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Section: Resultsmentioning

confidence: 99%

Quality assessment and preservation of RNA from biobank tissue specimens: a systematic review

2015

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“…Since the RNA integrity of several tissue types is not influenced by the freezing method 13 and morphology is not harmed, tissue banks may consider terminating the use of isopentane after further internal validation. However, for diagnostic purposes such as enzyme histochemistry on frozen sections of muscle biopsies, where optimal morphology is of crucial importance, it is still necessary to use isopentane for optimal results.…”

Section: Discussionmentioning

confidence: 99%

“…11 In a previous study, while the authors acknowledge the preservation effects of isopentane on morphology, it was not found to be better than nitrogen with respect to RNA quality. 13 Small samples such as needle biopsies can suffer air drying artifacts that damage tissue morphology and possibly also compromise RNA. To minimize evaporation, clinicians often send small samples to the laboratory either on moist gauze or submerged in isotonic salt solution.…”

Section: Introductionmentioning

confidence: 99%

The Influence of Tissue Procurement Procedures on RNA Integrity, Gene Expression, and Morphology in Porcine and Human Liver Tissue

Kap

Sieuwerts

Kubista

et al. 2015

Biopreservation and Biobanking

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The advent of molecular characterization of tissues has brought an increasing emphasis on the quality of biospecimens, starting with the tissue procurement process. RNA levels are particularly affected by factors in the collection process, but the influence of different pre-analytical factors is not well understood. Here we present the influence of tissue specimen size, as well as the transport and freezing protocols, on RNA quality. Large, medium, and smaller porcine liver samples were stored either dry, on moist gauze, or in salt solution for various times, and then frozen in either liquid nitrogen or in pre-cooled isopentane. Large and small human liver samples were frozen in pre-cooled isopentane either immediately or after one hour at room temperature. The small samples were stored dry, on moist gauze, or in salt solution. RNA was isolated and RIN values were measured. The RNA for six standard reference genes from human liver was analyzed by RT-qPCR, and tissue morphology was assessed for artifacts of freezing. Experiments using porcine liver samples showed that RNA derived from smaller samples was more degraded after one hour of cold ischemia, and that cooled transport is preferable. Human liver samples showed significant RNA degradation after 1 h of cold ischemia, which was more pronounced in smaller samples. RNA integrity was not significantly influenced by the transport or freezing method, but changes in gene expression were observed in samples either transported on gauze or in salt solution. Based on observations in liver samples, smaller samples are more subject to gene expression variability introduced by post-excision sample handling than are larger samples. Small biopsies should be transported on ice and snap frozen as soon as possible after acquisition from the patient.

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“…21,22 Our RIN values are similar to previously reported values for colon cancer tissue. 16,17 Whether tissue should be stored at -80°C or -140°C remains unclear. 13,23 We observed no adverse effects on RNA quality in fresh-frozen tissue after storage at -80°C for up to 6 years.…”

Section: Discussionmentioning

confidence: 99%

“…Four different quality groups can be distinguished based on the RIN result (RIN < 5: not reliable for downstream analysis, 5 < RIN < 6: reliable for RT-qPCR only, 6 < RIN < 8: reliable for RTqPCR and gene expression arrays, RIN > 8: high-quality RNA reliable for all downstream analyses). [15][16][17] …”

Section: Tissue Samplesmentioning

confidence: 99%

Impact of in Vivo Ischemic Time on RNA Quality—Experiences from a Colon Cancer Biobank

Olsen

Eiholm

et al. 2015

Biopreservation and Biobanking

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Considerable effort has been made to improve differentiated diagnostics as well as personalized treatment for colorectal cancer patients. High-quality fresh frozen tissue is often required to investigate relevant molecular signatures in these patients. In RNA expression studies, the "RNA integrity number" is widely accepted as a reliable marker of RNA quality. Here, we investigate the feasibility of obtaining high-quality tissue from a colon cancer biobank and the impact of in vivo ischemic time and various technical and clinicopathological factors on RNA quality. Biopsies were obtained immediately following the tumor removal. The time from clamping the main arterial supply to resection and removal of the tumor was used to estimate the in vivo ischemic time. We did not observe a significant difference in RNA quality between normal tissue and tumor tissue. We observed a significant correlation between in vivo ischemic time and RNA quality in normal tissue (r = -0.24, p<0.001) but not in tumor tissue. Male gender and laparoscopic procedure were also significantly associated with lower RNA quality in normal tissue only. In tumor tissue, poor differentiation was associated with low RNA quality. In conclusion, in vivo ischemic time, surgical procedure, and gender have minor but significant effects on the quality of RNA from normal colon tissue but not tumor tissue. Poorly differentiated tumors are associated with lower RNA quality. Although its impact is low, it can still be considered to note in vivo ischemic time in colon cancer specimen procurement.

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Fit for Purpose Frozen Tissue Collections by RNA Integrity Number-Based Quality Control Assurance at the Erasmus MC Tissue Bank

Cited by 42 publications

References 16 publications

Quality assessment and preservation of RNA from biobank tissue specimens: a systematic review

Quality assessment and preservation of RNA from biobank tissue specimens: a systematic review

The Influence of Tissue Procurement Procedures on RNA Integrity, Gene Expression, and Morphology in Porcine and Human Liver Tissue

Impact of in Vivo Ischemic Time on RNA Quality—Experiences from a Colon Cancer Biobank

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