Quantification of mRNA in whole blood by assessing recovery of RNA and efficiency of cDNA synthesis

BACKGROUND: Current gene expression analysis relies on the assumption that the isolated RNA represents all species of mRNA in proportions equal to those in the original materials. No system is available for absolute quantification of mRNA. METHODS: We applied whole blood to 96-well filterplates to trap leukocytes. Lysis buffer containing cocktails of specific reverse primers and known concentrations of synthetic external control RNA (RNA34) was added to filterplates, and cell lysates were transferred to oligo(dT)-immobilized microplates for hybridization. We then synthesized the cDNA in the oligo(dT)-immobilized microplates from these primer sites and used the cDNA for real-time PCR. RNA34 acted as a universal control, and gene amplification results were converted to quantities of mRNA per microliter of whole blood after the recovery of RNA34 in each sample was determined. RESULTS: Under fully optimized conditions, both added RNA34 and native mRNA species exhibited approximately 10% recovery from whole blood to real-time PCR. When whole blood was stimulated ex vivo, changes in gene expression as low as 30%-40% were detected with statistical significance, and the experimental CVs were low (10%-20%). CONCLUSION: This new system to estimate mRNA copies per microliter of whole blood may allow standardization of gene-expression-based molecular diagnostics.     

Detection of Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella spp. in clinical specimens using a single-tube multiplex real-time PCR assay

A multiplex real-time PCR assay for the detection of Mycoplasma pneumoniae (MP181), Chlamydia (Chlamydophila) pneumoniae (CP-Arg), Legionella spp. (Pan-Leg), and the human RNase P (RNase P) gene was developed for rapid testing of atypical bacterial respiratory pathogens in clinical specimens. This method uses 4 distinct hydrolysis probes to detect 3 leading causes of community-acquired pneumonia. The assay was evaluated for specificity and sensitivity by testing against 35 related organisms, a dilution series of each specific target and 197 clinical specimens. Specificity testing demonstrated no cross-reactivity. A comparison to previously validated singleplex real-time PCR assays for each agent was also performed. The analytical sensitivity for specific pathogen targets in both the singleplex and multiplex was identical (50 fg), while efficiencies ranged from 82% to 97% for the singleplex assays and from 90% to 100% for the multiplex assay. The clinical sensitivity of the multiplex assay was improved for the Pan-Leg and CP-Arg targets when compared to the singleplex. The MP181 assay displayed equivalent performance. This multiplex assay provides an overall improvement in the diagnostic capability for these agents by demonstrating a sensitive, high-throughput and rapid method. This procedure may allow for a practical and efficient means to test respiratory clinical specimens for atypical pneumonia agents in health care settings and facilitate an appropriate public health response to outbreaks.     

Expression level of MDR1 message in peripheral blood leukocytes from healthy adults: a competitive nucleic acid sequence-based amplification assay for its determination.

Accurate quantification of multidrug resistance-1 gene (MDR1) expression in target cells would be of important therapeutic value in predicting cellular response to anticancer drugs. Because certain normal cells in peripheral blood physiologically express MDR1, increasing the sensitivity of the detection methods might result in confounding low-degree expression in tumor cells with physiologic expression in normal cells. The purpose of this study was to determine MDR1 mRNA expression levels in peripheral blood leukocytes obtained from healthy adult volunteers using a competitive nucleic acid sequence-based amplification (NASBA) assay. We determined the reference intervals of MDR1 mRNA expression in peripheral blood obtained from 98 healthy adults by measuring its expression with the quantitative NASBA assay between 5.50 x 10(4) copies/microg RNA and 6.76 x 10(5) copies/microg RNA. The new reference intervals were evaluated using a number of sensitive or resistant cell lines as control; positive or negative MDR1 expression was clearly demonstrated. We also reevaluated MDR1 expression levels in leukemia cells obtained from patient peripheral blood; 18 of 31 samples (58%) exceeded the newly established upper reference limit. The cutoff value established could be used to distinguish significant MDR1 expression in tumor cells from physiologic expression in certain normal cells coexistent in peripheral blood.     

Improvement of real-time polymerase chain reaction for quantifying TNF-alpha mRNA expression in inflamed colorectal mucosa: an approach to optimize procedures for clinical use

OBJECTIVE: The precise measurement of local tumor necrosis factor alpha (TNF-alpha) expression in tissue is important in understanding the pathogenesis of inflammatory bowel diseases (IBD). Real-time polymerase chain reaction (PCR) is a sensitive, versatile method and is becoming a commonly used tool for the quantification of gene expression. The aim of this study was to optimize the laboratory procedure for biopsy sampling, storage and calibration of result for TNF-alpha mRNA quantification with real-time PCR of colorectal biopsies. MATERIAL AND METHODS: Endoscopic biopsies from the colorectum were obtained from 18 patients with ulcerative colitis (UC), 11 patients with Crohn's disease (CD) and 18 normal controls. Optimization of procedures for real-time PCR performance was carried out. RESULTS: The transport medium, RNAlater, exhibited a high preservation effect against RNA degradation even after 8 days of storage at room temperature; one biopsy from each patient was sufficient for RNA extraction, cDNA synthesis and TNF-mRNA quantification. An assay was established with a technical reproducible sensitivity of 100 copies/microL. The observed interassay variations were 7.4 % coefficient of variation (CV) and 7.2 % CV in low and high TNF-alpha mRNA expression biopsies, respectively. TNF-alpha mRNA levels in colorectal biopsies from patients with either CD or moderate to severe UC were markedly increased, and 8 approximately 9-fold higher than those in healthy controls. CONCLUSIONS: This optimization improves the clinical use of real-time PCR for quantification of TNF-alpha gene expression in colorectal biopsies and provides a sensitive reproducible assay.     

Single tube multiplex real-time PCR for the rapid detection of herpesvirus infections of the central nervous system

Human herpesvirus infection of immunocompromised hosts may lead to central nervous system (CNS) infection and diseases. In this study, a single tube multiplex real-time PCR was developed for the detection of five herpesviruses (HSV-1, HSV-2, VZV, EBV and CMV) in clinical cerebrospinal fluid (CSF) specimens. Two primer pairs specific for the herpesvirus polymerase gene and five hybridization probe pairs for the specific identification of the herpesvirus types were used in a LightCycler multiplex real-time PCR. A singleplex real-time PCR was first optimized and then applied to the multiplex real-time PCR. The singleplex and multiplex real-time PCRs showed no cross-reactivity. The sensitivity of the singleplex real-time PCR was 1 copy per reaction for each herpesvirus, while that of the multiplex real-time PCR was 1 copy per reaction for HSV-1 and VZV and 10 copies per reaction for HSV-2, EBV and CMV. Intra and inter-assay variations of the single tube multiplex assay were in the range of 0.02%–3.67% and 0.79%–4.35%, respectively. The assay was evaluated by testing 62 clinical CSF samples and was found to have equivalent sensitivity, specificity and agreement as the routine real-time PCR, but reducing time, cost and amount of used sample.     

相对定量RT-PCR法中内对照基因表达水平的稳定性及其应用评价

目的评价相对定量RT-PCR方法中不同内对照基因表达水平的稳定性及其对靶基因预后判断的影响程度。方法以36例食管癌患者为例,收集其手术前（B-1）、手术刚结束时（B0）和术后第三天（B＋3）的外周血样品。利用实时定量RT-PCR技术,分别检测内对照基因Beta-actin和GAPDH在不同时间的表达水平,并以CEA mRNA作为靶基因,比较基于这两种内对照得出的靶基因相对定量结果用于患者预后判断的差异;标准化的绝对定量结果被作为＂预后判断的参照标准＂。结果在三个取样时间点,两种内对照基因表达水平的标准偏差依次分别为Beta-actin mR-NA：1.44,1.56和1.92;GAPDH mRNA：3.16,3.28和4.04;两者的总体变异程度分别为9.9%和17.3%。术后一年的复发结果表明,绝对定量法和基于Beta-actin mRNA的相对定量法在预后判断中能够得到一致的结果,而GAPDH mRNA的相对定量结果与复发之间未显示统计学意义的相关性（P〉0.05）。结论相对定量RT-PCR法中内对照基因表达水平的变异程度低于10%时,才能保证内对照的有效性以及靶基因测定结果的可比性。基因表达研究时应对所用的内对照基因表达稳定性进行前期评估。     

VEGF-C mRNA和VEGFR-3 mRNA实时荧光定量检测方法的建立及初步应用

目的建立检测血管内皮生长因子-C（VEGF-C）mRNA和血管内皮生长因子受体-3（VEGFR-3）mRNA的实时荧光定量逆转录聚合酶链反应（FO-RT-PCR）方法,并在食管癌组织中作初步应用。方法采用TaqMan荧光探针技术,分别以pMD18-VEGF-C和pMD18-VEGFR-3质粒作为定量模板,应用循环阈值（Ct）定量起始模板,建立检测食管癌组织的VEGF-CmRNA和VEG—FR-3tuRNA的实时FQ-RT-PCR方法。结果所建方法的线性范围：VEGF-CmRNA和VEGFR-3mRNA均为10^3～10^8拷贝／μg总RNA;测定VEGF-C mRNA低值的批内、批间变异系数（CV）分别为7．07％和9．04％,测定VDGF-CmRNA高值的批内、批间CV分别为7．55％和10．28％;测定VEGFR-3mRNA低值的批内、批间CV分别为7．69％和12．49％,测定VEGFR-3mRNA高值的批内、批间CV分别为7．31％和9．17％。24例淋巴结转移食管癌患者癌组织VEGF-CmRNA和VEG—FR-3 mRNA的测定范围分别为3．69×10^4～9．44×10^6拷贝／μg总RNA和2．54×10^4～8．03×10^6拷贝／μg总RNA,均值分别为2．18×10^6拷贝／μg总RNA和2．27×10^6拷贝／μg总RNA。16例无淋巴结转移食管癌患者癌组织VEGF-CmRNA和VEGFR-3mRNA的测定范围分别为2．32×10^3～5．85×10^5拷贝／μg总RNA和7．31×10^2～8．21×10^4拷贝／μg总RNA,均值分别为1．08×10^5拷贝／μg总RNA和1．68×10^4拷贝／μg总RNA。提示有淋巴结转移的食管癌组织VEGF-C和VEG—FR-3基因表达水平上调。结论本组建立的检测VEGF-CmRNA和VEGFR-3mRNA的实时FQ-RT-PCR方法灵敏、准确、稳定、重复性好,可供VEGF-C、VEGFR-3基因表达的临床检测和研究应用。     

Determination of RhD zygosity: comparison of a double amplification refractory mutation system approach and a multiplex real-time quantitative PCR approach

BACKGROUND: Rh isoimmunization and hemolytic disease of the newborn still occur despite the availability of Rh immunoglobulin. For the prenatal investigation of sensitized RhD-negative pregnant women, determination of the zygosity of the RhD-positive father has important implications. The currently available molecular methods for RhD zygosity assessment, in general, are technically demanding and labor-intensive. Therefore, at present, rhesus genotype assessment is most commonly inferred from results of serological tests. The recent elucidation of the genetic structure of the prevalent RHD deletion in Caucasians, as well as the development of real-time PCR, allowed us to explore two new approaches for the molecular determination of RhD zygosity. METHODS: Two methods for RhD zygosity determination were developed. The first was based on the double Amplification Refractory Mutation System (double ARMS). The second was based on multiplex real-time quantitative PCR. For the double ARMS assay, allele-specific primers were designed to directly amplify the most prevalent RHD deletion found in RhD-negative individuals in the Caucasian population. The multiplex real-time quantitative PCR assay, on the other hand, involved coamplification and quantification of RHD-specific sequences in relation to a reference gene, albumin, in a single PCR reaction. A ratio, DeltaCt, based on the threshold cycle, was then determined and reflects the RHD gene dosage. RESULTS: The allele-specific primers of the double ARMS assay reliably amplified the RHD-deleted allele and therefore accurately distinguished homozygous from heterozygous RhD-positive samples. The results were in complete concordance with serological testing. For the multiplex real-time quantitative PCR assay, the DeltaCt values clearly segregated into two distinct populations according to the RHD gene dosage, with mean values of 1.70 (SD, 0.17) and 2.62 (SD, 0.29) for the homozygous and heterozygous samples, respectively (P: <0.001, t-test). The results were in complete concordance with the results of serological testing as well as with the double ARMS assay. CONCLUSION: Double ARMS and real-time quantitative PCR are alternative robust assays for the determination of RhD zygosity.