Biobanking of fresh-frozen human colon tissues: impact of tissue ex-vivo ischemia times and storage periods on RNA quality

Testing of tissue specimens obtained from SARS-CoV-2 nasopharyngeal swab-positive donors

Risk for transmission of SARS-CoV-2 through allogeneic human tissue transplantation is unknown. To further evaluate the risk of virus transmission, tissues were obtained from deceased donors who had tested positive for SARS-CoV-2 RNA via nasopharyngeal swab. This study evaluated an array of human tissues recovered for transplantation, including bone, tendon, skin, fascia lata, vascular tissues, and heart valves. Tissue samples and plasma or serum samples, if available, were tested for viral RNA (vRNA) using a real time PCR system for the presence of virus RNA. All samples were tested in quadruplicate for both subgenomic (sgRNA) and genomic (gRNA) RNA encoding the SARS-CoV-2 nucleocapsid gene. Amplification of a cellular housekeeping gene served as the positive control for every sample. A total of 47 tissue samples from 17 donors were tested for SARS-CoV-2 RNA. Four donors had plasma or serum available for paired testing. SARS-CoV-2 RNA was not detected from any tissue or plasma/serum sample tested. Based on these findings, risk of transmission through the transplantation of tissue types studied from SARS-CoV-2 infected donors is likely to be low.

Impact of Sample Processing and Storage Conditions on RNA Quality of Fresh-Frozen Cancer Tissues

Background: A biobank is a central resource that supports basic and clinical research. RNA quality of fresh-frozen tissue specimens in the biobank is highly associated with the success of downstream applications. Therefore, it is very important to evaluate the impact of tissue processing and storage conditions on RNA quality. Methods: A total of 238 surgically removed tissue specimens, including esophagus, lung, liver, stomach, colon, and rectal cancer, were used to evaluate RNA quality. Two tissue homogenization methods, manual and TissueLyser, were compared and the impacts of temperature fluctuation, tissue types, storage period, and clinicopathological parameters on RNA quality were analyzed. Results: RNA integrity was not influenced by tissue homogenization methods and tissue types. However, RNA integrity number (RIN) values were significantly correlated with temperature fluctuation. When the power of a -80°C freezer was cut off, RNA integrity of frozen tissues was not significantly affected until the temperature increased to 0°C. When the temperature rose to room temperature and remained for 4 hours, RNA integrity was almost completely destroyed. In addition, various cancer tissues with short-term storage at -80°C (<5 years) or high tumor differentiation had higher RINs. Conclusions: Tissue processing and storage conditions affected RNA quality of fresh-frozen cancer tissues. It is necessary to keep storage temperature stable and keep specimens at ultralow temperatures during homogenization. Also, for a biobank containing multiple types of cancer tissue samples, it is better to store them in liquid nitrogen if the storage duration is more than 5 years.

Standard operating procedures for the collection, processing, and storage of oral biospecimens at the Korea Oral Biobank Network

PURPOSE

The Korea Oral Biobank Network (KOBN) was established in 2021 as a branch of the Korea Biobank Network under the Korea Centers for Disease Control and Prevention to provide infrastructure for the collection, management, storage, and utilization of human bioresources from the oral cavity and associated clinical data for basic research and clinical studies.

METHODS

To address the need for the unification of the biobanking process, the KOBN organized the concept review for all the processes.

RESULTS

The KOBN established standard operating procedures for the collection, processing, and storage of oral samples.

CONCLUSIONS

The importance of collecting high-quality bioresources to generate accurate and reproducible research results has always been emphasized. A standardized procedure is a basic prerequisite for implementing comprehensive quality management of biological resources and accurate data production.

Quality Assessment of Cryopreserved Human Biological Samples from the Biobank of Barretos Cancer Hospital

Background: Biobanks process, store, and supply biological materials for research. Preanalytical factors, especially storage time and temperature, must be controlled and standardized at all stages when handling biospecimen samples, especially because the literature reports highly contradictory optimal parameters. As large-sample studies are required to better understand the influence of time and temperature on cryopreserved samples' quality for genomic research, this study evaluated the integrity and quality of cryopreserved samples stored for up to 9 years at the biobank of Barretos Cancer Hospital, one of the largest biobanks in Latin America. Methods: We randomly selected 447 samples with tumor tissue paired with buffy coat or peripheral blood mononuclear cells (PBMCs) that were stored from 2008 to 2016. The genetic material quality was evaluated based on RNA integrity (RIN) and DNA integrity (DIN) ≥7, which indicated undegraded samples, and compared with storage time, which means that for DNA storage time, samples <8.1 and ≥8.1 years and for RNA <4.5 and ≥4.5 were used. Results: A total of 190 tumor tissues were eligible for DNA and RNA extraction. Those stored for 8 years had lower DIN (68%) than those stored for a shorter period (92%). A similar pattern, based on storage time (<8.1 and ≥8.1 years), was observed in the buffy coat (74% and 95%, respectively) and PBMCs (54% and 96%, respectively). For RNA extracted from tumor tissues, we observed lower RIN in samples stored for 4.5 years (17%) than in samples stored for a shorter period (45%). Buffy coat and PBMC samples stored at -30°C exhibited greater degradation (26%) than those stored at -80°C (1%). The DIN (p = 0.15) and RNA (p = 0.18) were unrelated to topography type. Conclusion: The temperature, particularly cryopreservation methodology, and storage time were the main factors that affected nucleic acid integrity, especially RNA, during cryopreservation of biospecimens.

Impact of Washing Processes on RNA Quantity and Quality in Patient-Derived Colorectal Cancer Tissues

Background: Colorectal cancer (CRC) is a common and lethal cancer worldwide. Extraction of high-quality RNA from CRC samples plays a key role in scientific research and translational medicine. Specimen collection and washing methods that do not compromise RNA quality or quantity are needed to ensure high quality specimens for gene expression analysis and other RNA-based downstream applications. We investigated the effect of tissue specimen collection and different preparation processes on the quality and quantity of RNA extracted from surgical CRC tissues. Materials and Methods: After surgical resection, tissues were harvested and prepared with various washing processes in a room adjacent to the operating room. One hundred fourteen tissues from 36 CRC patients were separately washed in either cold phosphate-buffered saline reagent (n = 34) or Dulbecco's modified Eagle's medium (DMEM; n = 34) for 2-3 minutes until the stool was removed, and unwashed specimens served as controls (n = 34). Six tissue specimens were washed and immersed in DMEM for up to 1 hour at 4°C. Before RNA extraction, all specimens were kept in the stabilizing reagent for 3 months at -80°C. RNA was extracted, and the concentration per milligram of tissue was measured. RNA quality was assessed using the RNA integrity number (RIN) value. Results: Different washing processes did not result in significant differences in RNA quantity or RIN values. In the six tissues that were washed and immersed in DMEM for 1 hour, RIN values significantly decreased. The quality of the extracted RNA from most specimens was excellent with the average RIN greater than 7. Conclusions: RNA is stable in specimens washed in different processes for short periods, but RIN values may decrease with prolonged wash times.

Banking of Tumor Tissues: Effect of Preanalytical Variables in the Phase of Pre- and Postacquisition on RNA Integrity

Background: RNA integrity of tumor tissues from 12 common organs was measured, and tumor tissues from liver were found to have the best RNA integrity in our previous study. The effects of preanalytical variables in the phase of pre- and postacquisition on RNA integrity were further assessed in hepatocellular carcinoma (HCC) tissues in this study. Methods: RNA integrity number (RIN) was measured in tissues from 146 HCC patients. First, 42 fresh HCC tumor tissues were newly collected to assess the effect of various preanalytical variables in the phase of preacquisition on RNA integrity. Second, eight paired HCC tumor and normal tissues were newly collected and used in the gradient course study of ex vivo ischemia time and freeze-thaw cycles on RNA integrity. Finally, 96 stock-frozen tumor tissues with various years of frozen storage were used to assess the effect of cryopreservation time. Results: RNA integrity was found to be independent of patient age, sex, clinical stage, tumor location, HBV infection status, tumor diameter, and surgical approach, but affected by tumor grade. Tumor tissues with a greater tumor grade had lower RIN. With the prolongation of ex vivo ischemia time, freeze-thaw cycles, and cryopreservation time, the RIN of HCC tissues showed decreasing trends. Significant decreases in RIN of the tumor and normal tissues were observed at 6 and 2 hours of ex vivo ischemia time, respectively, and significantly decreased RIN of tumor tissues was observed after six freeze-thaw cycles and 6 years of cryopreservation. Conclusions: Preanalytical variables in the phase of preacquisition such as tumor grade, and in the postacquisition phase such as ex vivo ischemia time, freeze-thaw times, and freeze-storage time both have effects on RNA integrity of HCC tissues. Tissue-based translational research should pay attention to preanalytical variables when collecting and utilizing tumor tissues.

Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing

Background

Both RNA-Seq and sample freeze-thaw are ubiquitous. However, knowledge about the impact of freeze-thaw on downstream analyses is limited. The lack of common quality metrics that are sufficiently sensitive to freeze-thaw and RNA degradation, e.g. the RNA Integrity Score, makes such assessments challenging.

Results

Here we quantify the impact of repeated freeze-thaw cycles on the reliability of RNA-Seq by examining poly(A)-enriched and ribosomal RNA depleted RNA-seq from frozen leukocytes drawn from a toddler Autism cohort. To do so, we estimate the relative noise, or percentage of random counts, separating technical replicates. Using this approach we measured noise associated with RIN and freeze-thaw cycles. As expected, RIN does not fully capture sample degradation due to freeze-thaw. We further examined differential expression results and found that three freeze-thaws should extinguish the differential expression reproducibility of similar experiments. Freeze-thaw also resulted in a 3′ shift in the read coverage distribution along the gene body of poly(A)-enriched samples compared to ribosomal RNA depleted samples, suggesting that library preparation may exacerbate freeze-thaw-induced sample degradation.

Conclusion

The use of poly(A)-enrichment for RNA sequencing is pervasive in library preparation of frozen tissue, and thus, it is important during experimental design and data analysis to consider the impact of repeated freeze-thaw cycles on reproducibility.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07381-z.

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

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 a decrease in RIN, and the gene expressions of PI3KCB, AKT1, 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.

RNA-Integrity and 8-Isoprostane Levels Are Stable in Prostate Tissue Samples Upon Long-Term Storage at -80°C

Sampling of prostate tissue (n = 97) was performed in conjunction with planned radical prostatectomies, in collaboration with Biobank1^®. The tissue used in this study was collected during the period 2003-2016, quickly frozen, and kept at -80°C until assayed in 2018. RNA extraction was performed with two different protocols (miRNeasy and mirVana™), and RNA quality was determined by measuring the RNA Integrity Number (RIN). The level of isoprostanes is widely recognized as a specific indicator of lipid peroxidation both in vitro and in vivo. The level of 8-isoprostane was measured because it is the main oxidation product of arachidonic acid, the most abundant phospholipid fatty acid. The level of 8-isoprostane was measured using enzyme immunoassay. There was no statistically significant difference in yield between the samples isolated with the mirVana protocol compared to the miRNeasy protocol. Average RIN was 2.8 units higher with the mirVana extraction protocol compared to the miRNeasy protocol (p < 0.001). For miRNeasy extractions, RINs were 7.1 for prostatectomies in 2005-2007 and 6.2 for those in 2018 (p < 0.001). For mirVana extractions, the difference in RIN score between the two groups regarding years of collection was not statistically significant. There was no significant increase in the levels of 8-isoprostane between the 2005-2007 samples and the 2018. The conclusion is that there is no oxidation of phospholipids with increasing storage time up to 15 years.

Influence of Cold Ischemia Time and Storage Period on DNA Quality and Biomarker Research in Biobanked Colorectal Cancer Tissues

Objectives Biobanking plays an important role in future research. Assessment and control of the preanalytical variables of biobanked tissues are fundamentals for the optimal use of biospecimens. Methods Forty-five colorectal cancer (CRC) tissues stored at −80°C in Bio-Resource Bank were evaluated to define the influence of cold ischemia time (CIT) and storage period (SP) on DNA quality in biobanked tissues. Three CITs (less than 30 minutes (CIT-1), 30–45 minutes (CIT-2), and 45–60 minutes (CIT-3)) and three SPs (less than 1 year (SP-1), 2–3 years (SP-2), and 4–5 years (SP-3)) were chosen. NanoDrop spectrophotometer was used to determine the 260/280 ratio for DNA purity. DNA integrity was analyzed by a UV transilluminator following electrophoresis on 2% agarose gel. To evaluate the practical usability of DNA for biomarker research, KRAS mutation status was assessed by PCR amplification. Results All DNA specimens had a 260/280 ratio ranging between 1.8 and 2.0 with the exception of one specimen (CIT-2/SP-2 group). For DNA integrity, DNA appeared as a compact, high-molecular-weight band with no or scanty low-molecular-weight smears. The concordance of KRAS mutation status between paired biobanked frozen tissues and formalin-fixed paraffin-embedded tissues was 100%. DNA remained stable in CRC tissues kept at room temperature for up to 1 hour and long-term storage up to 5 years. Conclusions Storage conditions of our biobank are suitable for long-term (at least five years) specimen preservation with high DNA quality. These results have practical implications that could affect banking guidelines.

Impact of ischemia on sample quality of human pancreatic tissues

BACKGROUND

Successful clinical evaluation of human tumors relies on proper handling of tissue samples to maximally preserve the cellular and metabolic states in vivo. Pancreatic samples are particularly sensitive to sample mishandling due to the abundance of digestive enzymes. We study how the duration of ischemia, in vivo and ex vivo, both of which are unavoidable lagging periods following surgical dissection, significantly impact the utility of pancreatic samples.

METHODS

We systematically characterize a wide range of tissue integrity features, including histological patterns, cellular structures, DNA/RNA quality and activity of major signaling pathways in normal pancreases and pancreatic ductal adenocarcinoma (PDAC) tumor tissues from 41 patients with different ischemia.

RESULTS

We reveal that tissues experiencing longer periods of ischemia exhibit significant deterioration and could potentially mislead disease diagnosis and preclinical research. Based on these analyses, we propose an optimal procedure that balances better clinical practice and high tissue sample quality.

CONCLUSIONS

Our work provides a guideline for pancreatic sample handling and could have wide implications in clinical diagnosis and translational research.

Quality assessment of cryopreserved biospecimens reveals presence of intact biomolecules

Recapitulation of tumor features in isolated biomolecules is preeminently dependent on obtaining reliable quality biospecimen. Moreover, quality assessment of biobanked specimens at regular intervals is an essential intervention for carrying out effective translational and clinical research. In the current study, genomic DNA was extracted from 140 fresh frozen tissues of oral, breast and colorectal specimens cryopreserved over a period of 3 to 8 months (short term) and 3 to 4 years (long term). Quantification of genomic DNA by absorption and fluorescence spectroscopy confirmed high concentration while qualitative analysis by gel electrophoresis showed intact bands for 94% and 87% of short- and long-term cohorts, respectively. PC-LDA based classification of Raman spectra showed overlapping groups of both cohorts suggesting the quality of DNA being preserved irrespective of storage period. To the best of our knowledge this is the first Indian biobank study reporting quality analysis of biospecimens cryopreserved at different time periods.

In search of an evidence-based strategy for quality assessment of human tissue samples: report of the tissue Biospecimen Research Working Group of the Spanish Biobank Network

The purpose of the present work is to underline the importance of obtaining a standardized procedure to ensure and evaluate both clinical and research usability of human tissue samples. The study, which was carried out by the Biospecimen Science Working Group of the Spanish Biobank Network, is based on a general overview of the current situation about quality assurance in human tissue biospecimens. It was conducted an exhaustive review of the analytical techniques used to evaluate the quality of human tissue samples over the past 30 years, as well as their reference values if they were published, and classified them according to the biomolecules evaluated: (i) DNA, (ii) RNA, and (iii) soluble or/and fixed proteins for immunochemistry. More than 130 publications released between 1989 and 2019 were analysed, most of them reporting results focused on the analysis of tumour and biopsy samples. A quality assessment proposal with an algorithm has been developed for both frozen tissue samples and formalin-fixed paraffin-embedded (FFPE) samples, according to the expected quality of sample based on the available pre-analytical information and the experience of the participants in the Working Group. The high heterogeneity of human tissue samples and the wide number of pre-analytic factors associated to quality of samples makes it very difficult to harmonize the quality criteria. However, the proposed method to assess human tissue sample integrity and antigenicity will not only help to evaluate whether stored human tissue samples fit for the purpose of biomarker development, but will also allow to perform further studies, such as assessing the impact of different pre-analytical factors on very well characterized samples or evaluating the readjustment of tissue sample collection, processing and storing procedures. By ensuring the quality of the samples used on research, the reproducibility of scientific results will be guaranteed.

Impact of Cold Ischemic Time and Freeze-Thaw Cycles on RNA, DNA and Protein Quality in Colorectal Cancer Tissues Biobanking

Tissue-derived RNA, DNA and protein samples become more and more crucial for molecular detection in clinical research, personalized and targeted cancer therapy. This study evaluated how to biobanking colorectal tissues through examining the influences of cold ischemic time and freeze-thaw cycles on RNA, DNA and protein integrity. Here, 144 pairs of tumor and normal colorectal tissues were used to investigate the impact of cold ischemic times (0-48h) on RNA, DNA and protein integrity at on ice or room temperature conditions. Additionally, 45 pairs of tissues experienced 0-9 freeze-thaw cycles, and then the RNA, DNA and protein quality were analyzed. On ice, RNA, DNA and protein from colorectal tumor and normal tissues were all stable up to 48h after surgery. At room temperature, RNA in colorectal tumor and normal tissues began to degrade at 8h and 24h, respectively. Meanwhile, the tumor tissues DNA degradation occurred at 24h after surgery at room temperature. Similarly, the protein expression level of tumor and normal tissues began to change at 24h after the surgery at room temperature. Interestingly, tissue RNA and DNA remained stable even after 9 freeze-thaw cycles, whereas the proteins levels were remarkably changed after 7 freeze-thaw cycles. This study provided a useful evidence on how to store human colorectal tissues for biobanking. Preserving the surgical colorectal tissue on ice was an effective way to prevent RNA, DNA and protein degradation. Importantly, more than 7 repeated freeze-thaw cycles were not recommended for colorectal tissues.

How to preserve and handle fish liver samples to conserve RNA integrity

As transcriptomic studies are becoming more and more common, it is important to ensure that the RNA used in the analyses is of good quality. The RNA integrity may be compromised by storage temperature or freeze-thaw cycles, but these have not been well studied in poikilothermic fishes. This work studied the effects of tissue storage time and temperature, and freeze-thaw cycles of tissue and extracted RNA on RNA integrity in brown trout (Salmo trutta L.) liver. The storage time and temperature had an effect on RNA integrity, but RNA suitable for quantitative reverse transcription PCR (RT-qPCR) (RIN > 7) was still obtained from samples preserved at - 20 °C for 6 months. Freeze-thaw cycles of tissue or RNA did not compromise the integrity of RNA. RNA degradation had an effect on RT-qPCR results, and the effect depended on gene. The RT-qPCR analysis of historical samples from a bleached kraft pulp mill effluent exposure in 1984 revealed no significant cyp1a induction. Recommendations are given for the preservation and handling procedures of samples designated for transcriptomic analyses.

Audit of Quality and Quantity of Nucleic Acid Yield from Pediatric Acute Leukemia Cases Following a Bio-banking Initiative

Information which can be harvested from a biological sample has greatly improved with advancements in diagnostic technologies. However, in developing countries, the awareness about usefulness of bio-banking concept is lacking and centres which do offer it, depend mainly on - 20 or - 80 °C for sample storage due to lack of sophisticated infrastructure like vapour phase nitrogen storage preservation. Hence in these resource constraint settings, timely audit of quality of nucleic acids extractable from samples stored is of utmost importance. In this study, we explore the effect of - 20 °C storage over nucleic acids (DNA/RNA) isolated from blood samples of 180 patients with various leukaemia's following a bio-banking initiative. We observed that the integrity and quality of both DNA and RNA were maintained in 70 and 80% samples respectively over time as reflected by their concentration measurements and inherent uniform expression of housekeeping gene GAPDH. Only 3.7% of the RNA samples and 4.2% of the DNA samples yielded very low concentrations despite minimizing processing and technical loss. In nutshell, audit of our biobank sample yield highlights that storage of blood samples at - 20 °C does not compromise the fidelity of nucleic acids for future diagnostic and research work in a resource constraint setting.

RNA and DNA Integrity Remain Stable in Frozen Tissue After Long-Term Storage at Cryogenic Temperatures: A Report from the Ontario Tumour Bank

Background: It is widely assumed that the integrity of tissue specimens remains stable indefinitely if preserved at cryogenic temperatures. With biobanking reaching a level of maturity where samples are increasingly stored for 10 years and beyond, this assumption of prolonged stability should be tested. Data from such an assessment are critical to verify if samples stored for extended durations remain "fit for purpose" or if there is need to reconsider the utility of samples stored beyond a certain timeframe. The Ontario Tumour Bank has been collecting samples since 2004, and assesses a random selection of frozen samples each year for RNA and DNA integrity as a part of ongoing quality control (QC) practices. This historical quality assessment data provide a unique opportunity to assess the impact of extended storage on nucleic acid integrity using replicate samples that remain in the bank in the present day as comparators. Methods: To examine the stability of fresh-frozen tumor tissue stored at cryogenic temperatures, RNA was extracted and analyzed from 87 cases over 14 disease sites stored long term in vapor-phase liquid nitrogen (LN2) (approximately -180°C). Historical QC data were compared against new data after re-extraction of replicate samples to determine the effect of extended storage on RNA quality. In addition, DNA was extracted from a subselection of samples (n = 20) to determine the effect of prolonged storage on DNA integrity. Results: No time-dependent decrease in tissue RNA or DNA quality, as measured by RNA integrity number (RIN) and DNA integrity number, was observed over an 11-year period. As a secondary observation, RNA integrity was not predictive of DNA integrity: DNA quality may still be very good, and as such RIN scores should not be used as a substitute indicator for evaluating DNA. Conclusions: Extended cryogenic storage beyond 2-11 years remains a viable option for maintaining the high quality of specimens in biobanks.

Integration of Genomic and Transcriptional Features in Pancreatic Cancer Reveals Increased Cell Cycle Progression in Metastases

We integrated clinical, genomic, and transcriptomic data from 224 primaries and 95 metastases from 289 patients to characterize progression of pancreatic ductal adenocarcinoma (PDAC). Driver gene alterations and mutational and expression-based signatures were preserved, with truncations, inversions, and translocations most conserved. Cell cycle progression (CCP) increased with sequential inactivation of tumor suppressors, yet remained higher in metastases, perhaps driven by cell cycle regulatory gene variants. Half of the cases were hypoxic by expression markers, overlapping with molecular subtypes. Paired tumor heterogeneity showed cancer cell migration by Halstedian progression. Multiple PDACs arising synchronously and metachronously in the same pancreas were actually intra-parenchymal metastases, not independent primary tumors. Established clinical co-variates dominated survival analyses, although CCP and hypoxia may inform clinical practice.

Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project

The Functional Annotation of Animal Genomes (FAANG) project aims to identify genomic regulatory elements in both sexes across multiple stages of development in domesticated animals. This study represents the first stage of the FAANG project for the horse, Equus caballus. A biobank of 80 tissue samples, two cell lines and six body fluids was created from two adult Thoroughbred mares. Ante-mortem assessments included full physical examinations, lameness, ophthalmologic and neurologic evaluations. Complete blood counts and serum biochemistries were also performed. At necropsy, in addition to tissue samples, aliquots of serum, ethylenediaminetetraacetic acid (EDTA) plasma, heparinized plasma, cerebrospinal fluid, synovial fluid, urine and microbiome samples from all regions of the gastrointestinal and urogenital tracts were collected. Epidermal keratinocytes and dermal fibroblasts were cultured from skin samples. All tissues were grossly and histologically evaluated by a board-certified veterinary pathologist. The results of the clinical and pathological evaluations identified subclinical eosinophilic and lymphocytic infiltration throughout the length of the gastrointestinal tract as well as a mild clinical lameness in both animals. Each sample was cryo-preserved in multiple ways, and nuclei were extracted from selected tissues. These samples represent the first published systemically healthy equine-specific biobank with extensive clinical phenotyping ante- and post-mortem. The tissues in the biobank are intended for community-wide use in the functional annotation of the equine genome. The use of the biobank will improve the quality of the reference annotation and allow all equine researchers to elucidate unknown genomic and epigenomic causes of disease.

Tumor Cell Content and RNA Integrity of Surgical Tissues from Different Types of Tumors and Its Correlation with Ex Vivo and In Vivo Ischemia

BACKGROUND

Tissues from tumor patients are important resources for promoting cancer research, and therefore many biobanks have been established to collect tumor tissues; however, the quality of tumor tissues after surgical resection has not been well documented.

METHODS

A total of 896 cases of tissues from 12 types of tumors were chosen for this study. First, histopathological examination was conducted to evaluate the tumor cell content; second, microchip electrophoresis was used to determine the RNA integrity number (RIN) in 466 cases of tissues with a tumor cell content ≥ 75%; and, finally, a correlation test was used to analyze the effect of ischemia on RNA integrity in 384 cases of tissues with a recorded ischemia time.

RESULTS

Tumor tissues from 12 different organs had different tumor cell contents and RNA integrity. The liver had the highest percentage (69.7%) of tissue samples with a tumor cell content ≥ 75%, and the highest percentage (96%) of samples with an RIN ≥ 7. RNA integrity was not correlated with limited ex vivo ischemia time (5-60 min) in any of the 12 types of tumors. In contrast, a significant correlation with in vivo ischemia time was observed in several types of tumors.

CONCLUSIONS

Not every sample of excised tumor tissue has a sufficient amount of tumor cells and enough RNA integrity. In vivo ischemia has a more significant influence on RNA integrity, and tumor tissues have different tolerances to pre-analytical variables. Those conducting translational research should pay attention to pre-analytical variables when collecting and utilizing tumor tissues.

RNA and microRNA Stability in PAXgene-Fixed Paraffin-Embedded Tissue Blocks After Seven Years' Storage

OBJECTIVES

To evaluate the stability of RNA and microRNA (miRNA) in PAXgene-fixed paraffin-embedded tissue blocks after 7 years' storage.

METHODS

RNA and miRNA were extracted from PAXgene-fixed paraffin-embedded (PFPE) blocks in 2009 then stored at -80°C. Seven years later, RNA and miRNA were again extracted from the same blocks. RNA and miRNA integrity in the 2009 and 2016 extractions were compared using RNA integrity number (RIN), paraffin-embedded RNA metric (PERM), reverse transcription polymerase chain reaction (RT-PCR) for different amplicon lengths, and quantitative RT-PCR (qRT-PCR) for three mRNA and three miRNA targets.

RESULTS

In PFPE blocks, mRNA was poorer in 2016 extractions compared to the 2009 extractions in all blocks and all assays applied, with transcripts degrading at different rates in the same blocks. For miRNA, qRT-PCR showed no statistically significant differences between 2009 and 2016 extractions.

CONCLUSIONS

mRNA in PFPE tissue blocks degrades at room temperature storage over 7 years.

The role of the pathology department in the preanalytical phase of molecular analyses

After introducing the new molecules for the treatment of patients with tumoral pathology, the therapeutical decision will be taken depending on the molecular profile performed upon the harvested tissues. This major modification makes the molecular and morphological analysis an essential part in the clinical management of patients and the pathologist plays an important role in this process. The quality and reproducibility of the results are imperative today and they depend on both the reliability of the molecular techniques and the quality of the tissue we use in the process. Also, the genomics and proteomics techniques, used increasingly often, require high-quality tissues, and pathology laboratories play a very significant role in the management of all phases of this process. In this paper the parameters which must be followed in order to obtain optimal results within the techniques which analyze nucleic acids and proteins were reviewed.

Biobanking of Fresh-Frozen Cancer Tissue: RNA Is Stable Independent of Tissue Type with Less Than 1 Hour of Cold Ischemia

BACKGROUND

The effects of preanalytical variables in tissue processing and storage periods on RNA quality of tissues have been well documented in each type of cancer. However, few studies have been performed on a comparative assessment of the impacts across different cancer tissues, even though it is well known that RNase activity is highly variable in various tissue types and RNase-rich tissues have been found to yield low-quality RNA.

METHODS

We investigated the impacts of cold ischemia times and long-term storage on RNA integrity in various types of cancer tissue, which had been fresh-frozen and collected at the Samsung Medical Center Biobank. RNA quality was also evaluated with regard to histopathological variables. We analyzed RNA integrity number (RIN) data, which had been obtained from our quality control (QC) processes over the last 7 years. Approximately 2% of samples were randomly selected and processed to measure RIN quarterly and after 6 years of storage for QC purposes.

RESULTS

Fresh-frozen tumor tissues yielded high-quality RNA regardless of tumor type and histopathological features. Up to 1-hour cold ischemia times and up to 6-year storage times did not adversely influence RNA integrity. Only 3 samples showed RIN of <7 out of a total of 396 analyzed tumor tissues.

CONCLUSIONS

Tissue quality was not adversely affected by long-term storage or limited variations of cold ischemia times. The low-quality samples could be correlated with the structural composition or intratumoral heterogeneity of tissues. The strict application of standardized protocols for tissue collection is the key for high-quality biobanking.

Standardising RNA profiling based biomarker application in cancer-The need for robust control of technical variables

Histopathology-based staging of colorectal cancer (CRC) has utility in assessing the prognosis of patient subtypes, but as yet cannot accurately predict individual patient's treatment response. Transcriptomics approaches, using array based or next generation sequencing (NGS) platforms, of formalin fixed paraffin embedded tissue can be harnessed to develop multi-gene biomarkers for predicting both prognosis and treatment response, leading to stratification of treatment. While transcriptomics can shape future biomarker development, currently <1% of published biomarkers become clinically validated tests, often due to poor study design or lack of independent validation. In this review of a large number of CRC transcriptional studies, we identify recurrent sources of technical variability that encompass collection, preservation and storage of malignant tissue, nucleic acid extraction, methods to quantitate RNA transcripts and data analysis pipelines. We propose a series of defined steps for removal of these confounding issues, to ultimately aid in the development of more robust clinical biomarkers.

Multicenter fresh frozen tissue sampling in colorectal cancer: does the quality meet the standards for state of the art biomarker research?

The growing interest in the molecular subclassification of colorectal cancers is increasingly facilitated by large multicenter biobanking initiatives. The quality of tissue sampling is pivotal for successful translational research. This study shows the quality of fresh frozen tissue sampling within a multicenter cohort study for colorectal cancer (CRC) patients. Each of the seven participating hospitals randomly contributed ten tissue samples, which were collected following Standard Operating Procedures (SOP) using established techniques. To indicate if the amount of intact RNA is sufficient for molecular discovery research and prove SOP compliance, the RNA integrity number (RIN) was determined. Samples with a RIN < 6 were measured a second time and when consistently low a third time. The highest RIN was used for further analysis. 91% of the tissue samples had a RIN ≥ 6 (91%). The remaining six samples had a RIN between 5 and 6 (4.5%) or lower than 5 (4.5%). The median overall RIN was 7.3 (range 2.9-9.0). The median RIN of samples in the university hospital homing the biobank was 7.7 and the median RIN for the teaching hospitals was 7.3, ranging from 6.5 to 7.8. No differences were found in the outcome of different hospitals (p = 0.39). This study shows that the collection of high quality fresh frozen samples of colorectal cancers is feasible in a multicenter design with complete SOP adherence. Thus, using basic sampling techniques large patient cohorts can be organized for predictive and prognostic (bio)marker research for CRC.

Biobanking of fresh-frozen endoscopic biopsy specimens from esophageal adenocarcinoma

The process of preparing endoscopic esophageal adenocarcinoma samples for next-generation DNA/RNA sequencing is poorly described. Therefore, we assessed the feasibility and pitfalls of preparing esophageal adenocarcinoma endoscopic biopsies toward DNA/RNA samples suitable for next-generation sequencing. In this prospective study, four tumor biopsy samples were collected from consecutive esophageal cancer patients during esophagogastroduodenoscopy and fresh-frozen in liquid nitrogen. DNA and RNA were isolated from samples with a tumor percentage of at least 50%. For next-generation sequencing, double-stranded DNA (dsDNA) is required and high-quality RNA preferred. The quantity dsDNA and RNA quantity and quality were assessed with the Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Biopsy samples of 69 consecutive patients with esophageal adenocarcinoma were included. In five patients (7%), the tumor percentage was less than 50% in all four biopsies. Using a protocol allowing simultaneous DNA and RNA isolation, the median dsDNA yield was 2.4 μg (range 0.1-12.0 μg) and the median RNA yield was 0.5 μg (range 0.01-2.05 μg). The median RNA integrity number of samples that were fresh-frozen within 30 minutes after sampling was 6.7 (range 4.2-8.9) compared with 2.5 (1.8-4.5) for samples that were fresh-frozen after 2 hours. The results from this study show that obtaining dsDNA and RNA for next-generation sequencing from endoscopic esophageal adenocarcinoma samples is feasible. Tumor percentage and dsDNA/RNA yield and quality emphasize the need for sampling multiple biopsies and minimizing the delay before fresh-freezing.

Cryopreservation-Altered Expression of RNA and Protein Markers in Biological Specimens

The preservation of DNA, RNA, and protein markers in biological specimens is essential for initial diagnosis, subsequent verification, and comparison, as well as for archival retention of pathological materials in modern molecular diagnostics and precision medicine. Considerable attention has been paid to the methods of collection, handling, and preparation of specimens for initial testing, but insufficient attention to the long-term specimen preservation for later verification, comparison, and archival retention. In the present study, we have investigated the changes of expressions of RNAs and proteins in Hep-G2 cell specimens after cryopreservation at -80°C and in liquid nitrogen. Storage temperature and different cryoprotective agent (CPA) solutions not only affect cell viability but also more importantly the retention of various molecular markers after storage as detected by western blot and real-time fluorescent quantitative polymerase chain reaction. While the presence of CPAs increased the survival rates of cells after cryopreservation as expected, there was no consistent trend observed with regard to the RNA expression measurements. The data have significant implications with regard to the accuracy and interpretation of acquired data from specimens that have been cryopreserved without RNA and protein stabilization and point to the need for rethinking the assumptions, strategies, and criteria of optimizing biological specimen cryopreservation in molecular diagnostics.

Effects of Cold Ischemia on Gene Expression: A Review and Commentary

Frequently investigators request that tissues be collected and processed in less than one hour following removal from a patient. Some biorepositories expend significant personnel time and other resources in trying to meet such goals; however, it is unclear whether the perceived benefits of relatively short cold ischemia times warrant these added costs. The literature of human surgical tissues prospectively exposed to cold ischemia at several time points was reviewed to compare the changes in transcripts/genes and microRNA with time of cold ischemia. Also, reports of protein changes in response to cold ischemia were correlated to changes in genes. The literature is limited; however, for most tissues, only a small proportion of transcripts/genes (<1%) changes up to 3 hours following surgery and most transcripts increase rather than decrease in less than 2 hours of cold ischemia. Biorepositories and investigators must consider the literature for evidence of significant changes in molecular results from tissues before spending significant resources on relatively rapid collection of tissues to meet cold ischemia times of less than 3 hours. Instead, those using human tissues in research must consider if the cold ischemia times affect their use in specific research; hence are these tissues "fit for purpose?"

Quality Assurance of Samples and Processes in the Spanish Renal Research Network (REDinREN) Biobank

BACKGROUND

Biobanks are useful platforms to build bridges between basic, translational, and clinical research and clinical care. They are repositories of high-quality human biological samples ideal for evaluating their histological characteristics and also their genome, transcriptome, and proteome. The Spanish Renal Research Network Biobank contains more than 76,500 well-preserved frozen samples of a wide variety of kidney diseases, collected from 5450 patients seen by over 70 nephrology services throughout the Spanish territory.

OBJECTIVE

To determine and to report the results of the quality control of samples and processes conducted in our biobank, implemented in accordance with the requirements of the ISO 9001:2008 international standard.

STUDY DESIGN

Two types of quality controls were performed: (1) systematic, that is, measurement of viable peripheral blood mononuclear cells (PBMCs) obtained and purity of nucleic acids and (2) ad-hoc, that is, viability of thawed PBMC, DNA extraction process reproducibility, and the integrity and functionality of nucleic acids, implemented on a routine basis.

METHODS AND RESULTS

PBMC isolation by Ficoll yielded reproducible results and its cryopreserved viability was >90%. Acceptable A260/A280 ratios were obtained for the vast majority of the DNA (n = 2328) and RNA (n = 78) samples analyzed. DNA integrity was demonstrated by agarose gels and by β-globulin gene polymerase chain reaction (PCR) amplification of 1327 and 989 bp fragments. DNA of acceptable quality had at least three bands of β-globulin amplified obtained (n = 26/30). RNA integrity number (RIN) determinations obtained RIN numbers ≥7 (n = 87/96). The amplifiability of nucleic acids was confirmed by qPCR and RT-qPCR of β-actin and GAPDH genes. Long storage or delayed processing time did not affect the quality of the samples analyzed. The processes of DNA extraction also yielded reproducible results.

CONCLUSIONS

These results clearly indicate that our PBMC, DNA, and RNA stored samples meet the required quality standards to be used for biomedical research, ensuring their long-term preservation.

The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data

Successful molecular analyses of human solid tissues require intact biological material with well-preserved nucleic acids, proteins, and other cell structures. Pre-analytical handling, comprising of the collection of material at the operating theatre, is among the first critical steps that influence sample quality. The aim of this study was to compare the experimental outcomes obtained from samples collected and stored by the conventional means of snap freezing and by PAXgene Tissue System (Qiagen). These approaches were evaluated by measuring rRNA and mRNA integrity of the samples (RNA Quality Indicator and Differential Amplification Method) and by gene expression profiling. The collection procedures of the biological material were implemented in two hospitals during colon cancer surgery in order to identify the impact of the collection method on the experimental outcome. Our study shows that the pre-analytical sample handling has a significant effect on the quality of RNA and on the variability of qPCR data. PAXgene collection mode proved to be more easily implemented in the operating room and moreover the quality of RNA obtained from human colon tissues by this method is superior to the one obtained by snap freezing.

Assessment of clinically related outcomes and biomarker analysis for translational integration in colorectal cancer (ACROBATICC): study protocol for a population-based, consecutive cohort of surgically treated colorectal cancers and resected colorectal liver metastasis

Background

More accurate predictive and prognostic biomarkers for patients with colorectal cancer (CRC) primaries or colorectal liver metastasis (CLM) are needed. Outside clinical trials, the translational integration of emerging pathways and novel techniques should facilitate exploration of biomarkers for improved staging and prognosis.

Methods

An observational study exploring predictive and prognostic biomarkers in a population-based, consecutive cohort of surgically treated colorectal cancers and resected colorectal liver metastases. Long-term outcomes will be cancer-specific survival, recurrence-free survival and overall survival at 5 years from diagnosis. Beyond routine clinicopathological and anthropometric characteristics and laboratory and biochemistry results, the project allows for additional blood samples and fresh-frozen tumour and normal tissue for investigation of circulating tumour cells (CTCs) and novel biomarkers (e.g. immune cells, microRNAs etc.). Tumour specimens will be investigated by immunohistochemistry in full slides. Extracted DNA/RNA will be analysed for genomic markers using specific PCR techniques and next-generation sequencing (NGS) panels. Flow cytometry will be used to characterise biomarkers in blood. Collaboration is open and welcomed, with particular interest in mutual opportunities for validation studies.

Status and perspectives

The project is ongoing and recruiting at an expected rate of 120–150 patients per year, since January 2013. A project on circulating tumour cells (CTCs) has commenced, with analysis being prepared. Investigating molecular classes beyond the TNM staging is under way, including characteristics of microsatellite instability (MSI) and elevated microsatellite alterations in selected tetranucleotides (EMAST). Hot spot panels for known mutations in CRC are being investigated using NGS. Immune-cell characteristics are being performed by IHC and flow cytometry in tumour and peripheral blood samples. The project has ethical approval (REK Helse Vest, #2012/742), is financially supported with a Ph.D.-Grant (EMAST project; Folke Hermansen Cancer Fund) and a CTC-project (Norwegian Research Council; O. Nordgård). The ACROBATICC clinical and molecular biobank repository will serve as a long-term source for novel exploratory analysis and invite collaborators for mutual validation of promising biomarker results. The project aims to generate results that can help better discern prognostic groups in stage II/III cancers; explore prognostic and predictive biomarkers, and help detail the biology of colorectal liver metastasis for better patient selection and tailored treatment. The project is registered at http://www.ClinicalTrials.gov NCT01762813.

The effect of long-term -80°C storage of thyroid biospecimens on RNA quality and ensuring fitness for purpose

AIMS

To establish whether RNA degrades in long-term storage at -80°C and whether RNA integrity numbers (RINs) determine 'fitness for purpose' in severely degraded RNA.

METHODS

RNA was extracted from 549 thyroid biospecimens stored at -80°C for 0.1-10.9 years then their RINs correlated with storage time. RT-PCR for 65, 265, 534 and 942 base pair amplicons of hydroxymethylbilane synthase was used to measure amplicon length in RNA from cryopreserved and FFPE biospecimens that were equally degraded according to RIN.

RESULTS

Storage time did not correlate with RIN. Longer amplicons were obtained from cryopreserved samples than FFPE samples with equal RINs.

CONCLUSIONS

RNA does not degrade in thyroid biospecimens stored for long periods of time at -80°C. Although RINs are known to predict amenability to analytical platforms in good quality samples, this prediction is unreliable in severely degraded samples.

Biobanking of Fresh-Frozen Human Adenocarcinomatous and Normal Colon Tissues: Which Parameters Influence RNA Quality?

Medical research projects become increasingly dependent on biobanked tissue of high quality because the reliability of gene expression is affected by the quality of extracted RNA. Hence, the present study aimed to determine if clinical, surgical, histological, and molecular parameters influence RNA quality of normal and tumoral frozen colonic tissues. RNA Quality Index (RQI) was evaluated on 241 adenocarcinomas and 115 matched normal frozen colon tissues collected between October 2006 and December 2012. RQI results were compared to patients’ age and sex, tumor site, kind of surgery, anastomosis failure, adenocarcinoma type and grade, tumor cell percentage, necrosis extent, HIF-1α and cleaved caspase-3 immunohistochemistry, and BRAF, KRAS and microsatellites status. The RQI was significantly higher in colon cancer tissue than in matched normal tissue. RQI from left-sided colonic cancers was significantly higher than RQI from right-sided cancers. The RNA quality was not affected by ischemia and storage duration. According to histological control, 7.9% of the samples were unsatisfactory because of inadequate sampling. Biobanked tumoral tissues with RQI ≥5 had lower malignant cells to stromal cells ratio than samples with RQI <5 (p <0.05). Cellularity, necrosis extent and mucinous component did not influence RQI results. Cleaved caspase-3 and HIF-1α immunolabelling were not correlated to RQI. BRAF, KRAS and microsatellites molecular status did not influence RNA quality. Multivariate analysis revealed that the tumor location, the surgical approach (laparoscopy versus open colectomy) and the occurrence of anastomotic leakage were the only parameters influencing significantly RQI results of tumor samples. We failed to identify parameter influencing RQI of normal colon samples. These data suggest that RNA quality of colonic adenocarcinoma biospecimens is determined by clinical and surgical parameters. More attention should be paid during the biobanking procedure of right-sided colon cancer or laparoscopic colectomy specimen. Histological quality control remains essential to control sampling accuracy.

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

Introduction

Bio-repositories are invaluable resources to implement translational cancer research and clinical programs. They represent one of the most powerful tools for biomolecular studies of clinically annotated cohorts, but high quality samples are required to generate reliable molecular readouts and functional studies. The objective of our study was to define the impact of cancer tissue ischemia time on RNA and DNA quality, and for the generation of Patient-Derived Xenografts (PDXs).

Methods

One-hundred thirty-five lung cancer specimens were selected among our Institutional BioBank samples. Associations between different warm (surgical) and cold (ex-vivo) ischemia time ranges and RNA quality or PDXs engraftment rates were assessed. RNA quality was determined by RNA integrity number (RINs) values. Fresh viable tissue fragments were implanted subcutaneously in NSG mice and serially transplanted.

Results

RNAs with a RIN>7 were detected in 51% of the sample (70/135), with values of RIN significantly lower (OR 0.08, P = 0.01) in samples preserved for more than 3 hours before cryopreservation. Higher quality DNA samples had a concomitant high RIN. Sixty-three primary tumors (41 adenocarcinoma) were implanted with an overall engraftment rate of 33%. Both prolonged warm (>2 hours) and ex-vivo ischemia time (>10 hours) were associated to a lower engraftment rate (OR 0.09 P = 0.01 and OR 0.04 P = 0.008, respectively).

Conclusion

RNA quality and PDXs engraftment rate were adversely affected by prolonged ischemia times. Proper tissue collection and processing reduce failure rate. Overall, NSCLC BioBanking represents an innovative modality, which can be successfully executed in routine clinical settings, when stringent Standard Operating Procedures are adopted.

Pre-Analytical Determination of the Effect of Extended Warm or Cold Ischaemia on RNA Stability in the Human Ileum Mucosa

The use of banked human tissue, obtained with informed consent after elective surgical procedures, represents a powerful model for understanding underlying mechanisms of diseases or therapeutic interventions and for establishing prognostic markers. However, donated tissues typically have varying times of warm ischaemia in situ due to blood arrest or cold ischaemia due to procurement and transportation. Hence, before using these tissues, it is important to carry out pre-analytical studies to ensure that they are representative of the in vivo state. In particular, tissues of the gastrointestinal tract have been thought to have low RNA stability. Therefore, this study aimed to determine if extended warm or cold ischaemia times and snap-freezing or banking in RNA stabilization solution affects RNA integrity or gene expression in human ileum mucosa. In short, ileum mucosa was collected for up to 1.5 h and 6 h of simulated warm or cold ischaemia respectively. Subsequently, RNA integrity and gene expressions were determined. It was found that RNA integrity remained high over the course of warm and cold ischaemia examined and there were in general no significant differences between snap-freezing and banking in RNA stabilization solution. Following the same trend, there were in general no significant changes in gene expressions measured (MYC, HIF1α, CDX, HMOX1 and IL1β). In conclusion, RNA in the ileum mucosa is maintained at a high integrity and has stable gene expression over the examined time course of warm or cold ischaemia when banked in RNA stabilization solution or snap-frozen in liquid nitrogen. As the average warm and cold ischaemia times imposed by surgery and the process of tissue banking are shorter than the time period examined in this study, human ileum mucosa samples collected after surgeries could be used for gene expression studies.

Enriched Bone Marrow Derived Disseminated Neuroblastoma Cells Can Be a Reliable Source for Gene Expression Studies-A Validation Study

BACKGROUND

Metastases in the bone marrow (BM) in form of disseminated tumor cells (DTCs) are frequent events at diagnosis and also at relapse in high-risk neuroblastoma patients. The frequently highly diluted occurrence of DTCs requires adequate enrichment strategies to enable their detailed characterization. However, to avoid methodical artifacts we tested whether pre-analytical processing steps-including transport duration, temperature and, importantly, tumor cell enrichment techniques-are confounding factors for gene expression analysis in DTCs.

METHODS

LAN-1 neuroblastoma cells were spiked into tumor free BM and/or peripheral blood and: i) kept at room temperature or at 4°C for 24, 48 and 72 hours; ii) frozen down at -80°C and thawed; iii) enriched via magnetic beads. The effect on the gene expression signature of LAN-1 cells was analyzed by qPCR arrays and gene expression microarrays.

RESULTS

Neither storage at -80°C in DMSO and subsequent thawing nor enrichment of spiked-in neuroblastoma cells changed the expression of the analyzed genes significantly. Whereas storage at 4°C altered the expression of analyzed genes (14.3%) only at the 72h-timepoint in comparison to the 0h-timepoint, storage at room temperature had a much more profound effect on gene expression by affecting 20% at 24h, 26% at 48h and 43% at 72h of the analyzed genes.

CONCLUSION

Using neuroblastoma as a model, we show that tumor cell enrichment by magnetic bead separation has virtually no effect on gene expression in DTCs. However, transport time and temperature can influence the expression profile remarkably. Thus, the expression profile of routinely collected BM samples can be analyzed without concern as long as the transport conditions are monitored.

Establishment and management of a lung cancer biobank in Eastern China

Background

The prevalence of lung cancer, a highly complex neoplasm, increases annually. Thus, a lung cancer biobank, which stores lung cancer tissue and blood matched according to standard methods, is needed to advance lung cancer research and develop promising therapies.

Methods

To accomplish this aim, we implemented standardized procedures for tissue samples and patient information acquired from consenting donors. The banked tissue includes blood, pleural effusions, and surgical resection samples. An independent information management system was used to match samples and collect data, including clinical cancer manifestation, laboratory tests, and de-identified data about cancer patients.

Results

From 2009 to 2013, more than 2000 lung cancer cases were collected. At this time, we have more than 10 000 biological samples stored in our biobank. DNA, ribonucleic acid (RNA), and protein quality were confirmed to be appropriate for clinical and basic research.

Conclusion

Our standardized, large-scale lung cancer biobank offers high quality cancer research samples for China and the world.

Long-term storage of endocrine tissues at - 80°C does not adversely affect RNA quality or overall histomorphology

BACKGROUND

Today, no consensus exists regarding how human tissues are best preserved for long-term storage. Very low temperature storage in liquid nitrogen is often advocated as the superlative method for extended periods, but storage in -80 degrees Celsius (-80°C) freezers, while sometimes debated, is a possible alternative. RNA is the most easily degradable component of a biological sample in a molecular biology context and the quality can reliably be measured.

AIM

To investigate to what extent long-term storage of tissues in -80°C affects the RNA quality and overall histomorphology. The tissue storage period represents nearly three decades (1986-2013).

METHODS

RNA extraction from 153 tissue samples with different storage periods was performed with the mirVana kit (Invitrogen). RNA integrity was assessed using an Agilent bioanalyzer to obtain RNA integrity numbers (RIN). Further, tissue representative testing using light microscopy was performed by two pathologists to assess tissue composition and morphology.

RESULTS

RIN values were measured in all samples, showing a variability that did not correlate with the storage time of the tissues. Microscopically, all samples displayed acceptable tissue morphology regardless of storage time.

CONCLUSION

Long-term storage in -80°C does not adversely affect the quality of the RNA extracted from the stored tissues, and the tissue morphology is maintained to a good standard.

World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonisation Project: IV. Tissue collection, processing, and storage in endometriosis research

OBJECTIVE

To harmonize standard operating procedures (SOPs) and standardize the recording of associated data for collection, processing, and storage of human tissues relevant to endometriosis.

DESIGN

An international collaboration involving 34 clinical/academic centers and three industry collaborators from 16 countries on five continents.

SETTING

In 2013, two workshops were conducted followed by global consultation, bringing together 54 leaders in endometriosis research and sample processing from around the world.

PATIENT(S)

None.

INTERVENTION(S)

Consensus SOPs were based on: 1) systematic comparison of SOPs from 24 global centers collecting tissue samples from women with and without endometriosis on a medium or large scale (publication on >100 cases); 2) literature evidence where available, or consultation with laboratory experts otherwise; and 3) several global consultation rounds.

MAIN OUTCOME MEASURE(S)

Standard recommended and minimum required SOPs for tissue collection, processing, and storage in endometriosis research.

RESULT(S)

We developed "recommended standard" and "minimum required" SOPs for the collection, processing, and storage of ectopic and eutopic endometrium, peritoneum, and myometrium, and a biospecimen data collection form necessary for interpretation of sample-derived results.

CONCLUSION(S)

The EPHect SOPs allow endometriosis research centers to decrease variability in tissue-based results, facilitating between-center comparisons and collaborations. The procedures are also relevant to research into other gynecologic conditions involving endometrium, myometrium, and peritoneum. The consensus SOPs are based on the best available evidence; areas with limited evidence are identified as requiring further pilot studies. The SOPs will be reviewed based on investigator feedback and through systematic triannual follow-up. Updated versions will be made available at: http://endometriosisfoundation.org/ephect.

Superficial scrapings from breast tumors is a source for biobanking and research purposes

Breast cancer is a unique tumor disease in terms of the stringent requirement of predictive biomarker assessments. As recommended by current international guidelines, the established markers consist of estrogen receptor (ER), progesterone receptor, human epidermal growth factor and Ki67, and are primarily analyzed by immunohistochemistry. However, new diagnostic methods based on microarray or next-generation sequencing on DNA and mRNA level are gaining ground. These analyses require fresh-frozen tumor tissue that is generally not available from tumors <10 mm in diameter, comprising almost 25% of all resected breast cancer at our department. We here present a simple and standardized method to generate material from small tumors without risking the histopathological examination. Furthermore, we show that the quality of this material is sufficient for subsequent analysis on mRNA, DNA, and epigenetic level. We were also able to use this method for isolation and expansion of cancer stem cells from the majority of tumors. Consequently, researches can be provided with clinically relevant material for translational studies. In conclusion, this method opens up a new possibility for usage of valuable fresh tumor material for research purposes, biobanking, and next-generation sequencing.