Preanalytical aspects of quantitative TaqMan real-time RT-PCR: applications for TF and VEGF mRNA quantification

OBJECTIVES: The present paper focuses on preanalytical aspects of tissue factor (TF) and vascular endothelial growth factor (VEGF) mRNA quantification: the choice of blood collection tubes and defining the time frame allowed before processing the sample. DESIGN AND METHODS: Blood was collected from healthy volunteers in K(3) EDTA tubes, CPT, endotoxin-free EndoTube tubes and in PAXgene tubes. Total RNA concentration was determined by absorbance readings at 260 nm with a GeneQuantII UV spectrophotometer. RNA quantity and quality were also determined by the Lab on a Chip technique (Agilent 2100 Bioanalyzer). Real-time RT-PCR assays were performed by the TaqMan technology. RESULTS: The more expensive PAXgene and CPT tubes and the Endo tubes did not give superior results from those obtained in inexpensive routine K(3) EDTA tubes. The PAXgene tubes preserved high molecular mass rRNA better than the other tubes. CONCLUSION: Both the PAXgene system and routine EDTA tubes are suitable for clinical purposes aimed at quantitation of mRNA for TF and VEGF. PAXgene yielded rRNA that was less degraded but had lower mRNA per microg extracted RNA. A time frame up to 24 h until sample processing is acceptable for TF and VEGF mRNA.     

Optimization of the PAXgene blood RNA extraction system for gene expression analysis of clinical samples

One major problem associated with collecting whole blood from patients for use as a source of RNA in gene expression studies is that the RNA degrades during collection and storage. Preservation of RNA quality is vital in such studies because the stability of the RNA ultimately affects analysis of gene expression. In this study the PAXgene blood collection system was compared with a standard erythrocyte lysis method for isolating RNA from blood samples. The methods were compared in terms of RNA yield, RNA stabilization, and DNA contamination. The study also included the downstream application to RT-PCR analysis for relative mRNA expression levels of the ribonucleotide reductase subunits R1 and R2. The results show that blood collection in conventional collection tubes, and leukocyte isolation by erythrocyte lysis lead to significant degradation of RNA. Our findings confirm the ability of PAXgene to stabilize RNA in whole blood; however, RNA extracted by the PAXgene method contained significant DNA contamination. Given the low basal expression of the target genes analyzed in this study, contaminating DNA could potentially affect accurate interpretation of RT-PCR data. As a result, the PAXgene protocol was optimized to include off-column DNase treatments, which yielded high-quality RNA suitable for gene expression studies. Furthermore, the results suggest that RNA isolation with PAXgene is advantageous compared to traditional extraction methods for RT-PCR analysis of large or different-sized amplicons.     

Effects of temperature on stability of blood homocysteine in collection tubes containing 3-deazaadenosine

BACKGROUND: The accuracy of homocysteine (Hcy) results is currently compromised by the requirement to separate the plasma within 1 h of sample collection. We studied the effect of temperature on the stability of plasma Hcy over a 72-h time course in blood collected into evacuated tubes containing either EDTA alone or both EDTA and 3-deazaadenosine (3DA). METHODS: We recruited 100 volunteers, including both diseased and healthy individuals with a range of baseline plasma Hcy values, from two centers. Blood samples were collected into tubes containing EDTA, and EDTA plus 3DA and stored at ambient temperature (20-25 degrees C) or refrigerated (2-8 degrees C). Aliquots of blood were centrifuged at various times up to 72 h, the plasma was removed, and Hcy was measured by HPLC. RESULTS: Plasma Hcy measurement covering the sample collection and storage conditions during the whole time course was possible on samples from 59 of those recruited. One-way ANOVA for repeated measures within subjects revealed that only samples that were collected into tubes containing EDTA plus 3DA and stored refrigerated were stable over 72 h (P = 0.2761). CONCLUSIONS: A combination of 3DA and storage at 2-8 degrees C will allow collection of samples for plasma Hcy measurement outside of the hospital setting and wider population screening.     

Optimizing RNA extraction yield from whole blood for microarray gene expression analysis

OBJECTIVES: Microarray analysis of gene expression profiles of blood leukocytes has many potential clinical and research applications. DESIGN AND METHODS: We used the PAXgene Blood RNA System to prepare RNA from the whole blood of normal volunteers using two incubation times followed by gene expression profiling using the Affymetrix HU133A GeneChip. CONCLUSIONS: Longer incubation gave a significantly higher RNA yield and samples that were satisfactory for microarray analysis, with excellent pairwise correlations between replicates.     

Effect of collection tube type and preanalytical handling on myeloperoxidase concentrations

BACKGROUND: Myeloperoxidase (MPO) has shown potential as a marker for cardiovascular disease. Limited studies have been published with a variety of sample types, resulting in a wide range of MPO values. Little is known or understood about the impact of collection tube type and preanalytical handling of specimens for MPO determination. METHOD: MPO concentration was determined by use of the ARCHITECT(R) MPO research use assay, which is currently under development. Samples were collected into multiple anticoagulant collection tubes from donors and patients presenting to the emergency department with symptoms of acute coronary syndromes. Whole blood was stored on ice or at room temperature for predetermined time periods. We also evaluated serum and plasma after centrifugation followed by storage at room temperature, 2-8 degrees C, and below -10 degrees C. RESULTS: Baseline sample concentrations were dependent on collection tube type as well as handling conditions. MPO concentrations were consistently higher in samples collected in serum and heparin plasma tubes than in samples in EDTA or citrate tubes. Spike recovery was acceptable in all sera and plasma tested, indicating that the increased MPO concentrations were not due directly to an anticoagulant interference. CONCLUSIONS: The collection tube type and preanalytical handling are critical for accurate and consistent MPO measurement. The preferred anticoagulant and tubes are the EDTA or EDTA plasma preparation tube. MPO concentrations in samples collected in these tubes are stable before centrifugation as whole blood as well as plasma after processing.     

Optimal conditions for collection of blood samples for assay of α2-macroglobulin trypsin complex-like substance (MTLS)

We have developed an enzyme-linked immunosorbent assay (ELISA) for the specific quantification of α2-macroglobulin-trypsin complex-like substance (MTLS). To exclude artifacts in measured values of MTLS, the conditions for collection of blood samples are critical. In the present study, we have determined the optimal conditions for blood collection and investigated the role of MTLS as a clinical tool for diagnosis in pancreatitis. Results obtained are as follows: (1) MTLS levels of all sera were more than 10-fold higher than the corresponding plasma; (2) MTLS levels of heparinized plasma were the lowest among plasma with three anticoagulants (sodium citrate, sodium EDTA and heparin); (3) some kinds of blood collection tubes containing heparin were not suitable for the sampling; (4) MTLS values of plasma obtained by blood collection tubes containing Trasylol® and sodium EDTA were demonstrated more stable and lower than those obtained by heparin tubes; and (5) under these conditions, we can exclude elevation of MTLS values caused by inappropriate blood sampling and find the time course of the elevation reflecting clinical course of a patient with acute pancreatitis and a patient after endoscopic retrograde cholangiopan-creatography (ERCP). The optimal conditions for collection of blood samples were as follows. Blood sampling should be performed by blood collection tubes containing Trasylol® (50 μl/ml blood) and sodium EDTA (1.5 mg/ml blood). The samples were immediately stored at 4°C and centrifuged at 3,000 rpm for 15 min. The plasma were stored in plastic tubes at 4°C until assayed. © 1996 Wiley-Liss, Inc.     

Preanalytical mRNA stabilization of whole bone marrow samples

BACKGROUND: Gene expression profiling is a useful tool for cancer diagnosis and basic research. A major limitation is that, even during short-term storage of native specimens of peripheral blood or bone marrow (BM) and/or RNA isolation, significant changes of gene expression pattern can occur because of gene induction, repression, and RNA degradation. METHODS: We investigated the effectiveness of a newly developed RNA stabilization and preparation system for BM specimens (PAXgene Bone Marrow RNA System) over time. We analyzed 256 RNA samples, processed from 64 BM specimens. RESULTS: Although the overall RNA yield (normalized to 1 x 10(7) leukocytes) was not different, the RNA preparation using unstabilized reference samples had an approximately 3 times higher failure rate. With the PAXgene system, we observed significantly higher RNA integrity compared with the reference RNA preparation system (P <0.01). In the stabilized samples, we found very high pairwise correlation in gene expression (DeltaDeltaC(T) 0.16-0.53) for the analyzed genes (GATA1, RUNX1, NCAM1, and SPI1) after 48-h storage compared with immediate preparation of RNA (2 h after BM collection). However, we found major differences in half of the analyzed genes using the reference RNA isolation procedure (DeltaDeltaC(T) 1.07 and 1.32). CONCLUSIONS: The PAXgene system is able to stabilize RNA from clinical BM samples and is suitable to isolate high-quality and -quantity RNA.     

A stabilizing reagent prevents cell-free DNA contamination by cellular DNA in plasma during blood sample storage and shipping as determined by digital PCR

Objectives

To study the ability of a stabilizing reagent to prevent cellular DNA contamination of cell-free DNA (cfDNA) in plasma during whole blood sample storage and shipping.

Design and methods

Samples were drawn from healthy donors into K₃EDTA and Cell-Free DNA BCTs (BCT) and stored at room temperature (RT). Aliquots were removed at specified time points and cfDNA was purified from the plasma. A Droplet Digital PCR (ddPCR) assay that amplifies a short β-actin gene fragment (136 bp) was used to measure the total plasma cfDNA (pDNA) concentration while a longer β-actin fragment (420 bp) was used to quantify genomic DNA (gDNA). In a follow-up experiment, blood samples drawn into the same types of tubes were shipped round trip by overnight air before cfDNA was isolated and analyzed.

Results

Blood stored in K₃EDTA tubes at RT showed increases in pDNA and gDNA concentrations over time. However, both pDNA and gDNA levels remained stable in BCT for at least seven days. On day 14, there was a 4.5-fold increase in pDNA in BCT as compared to > 200-fold increase in K₃EDTA tubes. Likewise, gDNA increased < 2-fold on day 14 in BCT as opposed to a 456-fold increase in K₃EDTA tubes. Similar results were observed after samples were shipped.

Conclusions

Cell-Free DNA BCTs prevent gDNA contamination that may occur due to nucleated cell disruption during sample storage and shipping. This novel blood collection tube provides a method for obtaining stable cfDNA samples for rare target detection and accurate analysis while mitigating the threat of gDNA contamination.     

血浆同型半胱氨酸及其相关硫醇物在全血中的稳定性研究

目的 观察含EDTA的全血样本放置时间、保存温度以及不同稳定剂对血浆同型半胱氨酸(homocysteine,Hcy)及其相关硫醇物水平的影响.方法 用含EDTA、EDTA-氟化钠(EDTA-NaF)、EDTA-3-Deazaadenosine(EDTA-3DA)的试管收集17名健康成人静脉血,置于碎冰上(0～4 ℃)或室温中(25 ℃)保存,放置0、3、6、24、48 h后分离血浆.用HPLC法测定血浆总同型半胱氨酸(tHcy)、总半胱氨酸(total cysteine,tCys)、总半胱氨酰甘氨酸(total cysteinylglycine,tCysGly)、总谷胱甘肽(total glutathione,tGSH)浓度.设定全血样本0 h分离血浆所测硫醇物浓度为基础值.结果 EDTA管在室温中放置3、6、24、48 h,tHcy分别增加38.5%、64.2%、141.9%、225.4%;tCysGly、tGSH在3 h分别增加20.0%、37.9%,tCys则降低3.5%.EDTA管在碎冰上保存,各硫醇物浓度6 h内增加不超过5%.EDTA-3DA和EDTA-NaF管在室温放置3 h,与各自基础值相比,血浆tHcy、tCys、tCysGly、tGSH浓度差异无统计学意义(EDTA-3DA管:F值分别为0.01、0.94、0.09、0.01,P值均>0.05;EDTA-NaF管:F值分别为0.85、0.04、0.03、0.02,P值均>0.05).结论 EDTA抗凝血浆,所测tHcy及其相关硫醇物浓度呈时间、温度依赖性增加.血浆tHcy等硫醇物测定的分析前处理条件必须标准化.EDTA-3DA和EDTA-NaF管可使血浆tHcy、tCys、tCysGly、tGSH在室温中至少稳定3 h.

Abstract：

Objective To investigate the effects of different stabilizers, time and temperature before centrifugation on the stability of homocysteine (Hcy) and other related thiols levels involving EDTA-containing whole blood.Methods Blood was drawn from 17 healthy adults and collected into tubes containing EDTA, EDTA plus NaF and EDTA plus 3-deazaadenosine(3DA),then stored on crush ice(0-4 ℃) immediately or at room temperature(25 ℃).Plasma was separated at 0, 3, 6, 24 and 48 hours, respectively.The levels of plasma total Hcy (tHcy), total cysteine (tCys), tatal cysteinylglycine (tCysGly) and tatal glutathione (tGSH) were measured by HPLC.The plasma immediately separated was used as baseline sample. Results In EDTA tubes stored at room temperature, tHcy levels increased by 38.5%, 64.2%, 141.9%, 225.4% for 3, 6, 24, and 48 h, respectively.The levels of tCysGly and tGSH increased by 20.0% and 37.9% within 3 h, however, tCys decreased by 3.5%.The levels of the thiols increase by less than 5% up to 6 h in EDTA tubes stored on crush ice.In EDTA-3DA and EDTA-NaF tubes, no statistical differences were observed in the plasma levels of tHcy, tCys,tCysGly and tGSH compared with their respective baseline values at room temperature for 3 h(EDTA-3DA tubes:F=0.01,0.94,0.09,0.01,all P>0.05;EDTA-NaF tubes:F=0.85,0.04,0.03,0.02,all P>0.05).Conclusions The EDTA-plasma levels of tHcy and other related thiols are time and temperature-dependent. There is a strong need for standardization of blood sample collection and processing in tHcy and other thiols assays. The plasma concentrations of tHcy, tCys, tCysGly and tGSH were stable for 3 h at least in the EDTA-3DA and EDTA-NaF tubes kept at room temperature.     

Isolation of microarray-grade total RNA, microRNA, and DNA from a single PAXgene blood RNA tube

We have developed a procedure for isolation of microRNA and genomic DNA in addition to total RNA from whole blood stabilized in PAXgene Blood RNA tubes. The procedure is based on automatic extraction on a BioRobot MDx and includes isolation of DNA from a fraction of the stabilized blood and recovery of small RNA species that are otherwise lost. The procedure presented here is suitable for large-scale experiments and is amenable to further automation. Procured total RNA and DNA was tested using Affymetrix Expression and single-nucleotide polymorphism GeneChips, respectively, and isolated microRNA was tested using spotted locked nucleic acid-based microarrays. We conclude that the yield and quality of total RNA, microRNA, and DNA from a single PAXgene blood RNA tube is sufficient for downstream microarray analysis.     

不同处理和保存条件下体外HCV RNA稳定性研究

对献血者或病人进行HCV核酸检测时，如果标本的采集、处理、保存不当，会造成病毒核酸降解，从而影响检测结果的真实性。本研究的目的是对不同抗凝剂、不同温度、不同保存时间下的HCV RNA病毒稳定性进行研究，以考察常规采供血过程中，标本采集及保存方式对NAT检测的影响。采集7例HCV RNA阳性献血者的血样，采用不同的抗凝剂、经不同的温度和不同的时间保存后，采用荧光定量PCR方法测定HCV RNA病毒含量，考察HCV RNA的稳定性。结果表明：①不同抗凝剂抗凝的全血于4℃保存48小时过程中，病毒含量下降至原滴度的42．7％；EDTA抗凝组各时间点的滴度均低于其它3组（分别相当于其它3组的67．6％-25．1％）。②ACD抗凝的全血在4、25和37℃保存48小时．病毒含量分剐下降到原滴度的53．8％、72．5％、29．8％。③ACD抗凝的全血离心分离出血浆，4℃或25℃继续保存7天，病毒含量分别下降至原滴度的70．9％和25．1％。④ACD抗凝的全血分离的血浆，反复冻融4次，病毒含量下降到原滴度的38．9％。结论：①用于核酸检测的标本应该用无菌采血管采样；②在无菌采血管采样的前提下，核酸检测标本用未抗凝血、EDTA、ACD、CPDA抗凝血均可；③采集的全血应避免放置37℃以上，ACD抗凝全血在4℃、25℃保存48小时内、37℃保存14小时内，HCV RNA病毒仍较为稳定；④分离后的血浆应避免放置25℃以上，ACD抗凝全血分离后的血浆在4℃保存7天，25℃保存3天，HCV RNA病毒仍比较稳定；⑤血浆标本应避免多次冻融，但冻融3次的血浆HCV RNA病毒含量仍然较为稳定；⑥无菌采样对维持病毒的稳定性非常重要；单纯的机械性溶血并不会明显导致病毒的降解；只要注意无菌的问题和有合适的核酸提取方法去除血红素，HCV RNA病毒实际上比以前认为的要稳定得多。