Quantification of relative changes in specific mRNAs from frozen whole blood - methodological considerations and clinical implications.

BACKGROUND: Based on quantification of relative changes in lipopolysaccharide (LPS)-regulated mRNA transcripts, the present study aimed to establish a robotic method to isolate RNA from stabilized frozen whole blood suitable for gene expression analysis. METHODS: Whole blood (+/-LPS) was stored in EasyLyse solution or PAXgene tubes (room temperature and -70 degrees C) for comparison of storage methods, then subjected to robotic isolation of total RNA. Yield, quality and relative changes in 11 selected mRNA transcripts were examined. Method precision (% coefficient of variation) for a longitudinal control was established. The influence of globin mRNA from reticulocytes in quantitative RT-PCR was examined. RESULTS: All storage methods gave a similar high-quality RNA yield. The differences in the 11 specific mRNA quantities stored in EasyLyse or PAXgene at -70 degrees C were small: mean -0.01 (95% CI -0.19 to 0.17). The CV for mRNAs in the longitudinal control ranged from 3% to 150%. Thus, the number of replicates necessary to detect a 20% difference (power 0.8) ranged from 2-50. Globin mRNA had no influence on quantitative RT-PCR. CONCLUSIONS: Based on measuring the relative changes in specific mRNAs in LPS-exposed whole blood, we conclude that PAXgene tubes stored at -70 degrees C could preferentially be used. This may open opportunities for monitoring gene expression changes in clinical settings.

Use of robotized DNA isolation and real-time PCR to quantify and identify close correlation between levels of Neisseria meningitidis DNA and lipopolysaccharides in plasma and cerebrospinal fluid from patients with systemic meningococcal disease.

The present study, using robotized DNA isolation and quantitative PCR based on the Neisseria meningitidis-specific capsular transport A gene, demonstrates the ease, rapidity, specificity, and sensitivity of quantifying neisserial DNA in plasma (n = 65) and cerebrospinal fluid (CSF) (n = 12) from patients with systemic meningococcal disease. We found a close correlation between the levels of neisserial DNA and lipopolysaccharides in plasma (r = 0.905) and in CSF (r = 0.964). The median concentration of neisserial DNA in plasma in 23 patients with persistent shock was 2 x 10(7) copies/ml, versus <10(3) copies/ml in 42 nonshock patients. Furthermore, quantitative PCR made possible estimates of the total number of meningococci in plasma, as opposed to conventional blood cultures, suggesting about 1,000 dead meningococci for every viable bacterium. Finally, with logistic regression analyses, neisserial DNA may predict a patient's disease severity and outcome at hospital admission. The number of meningococci in plasma and CSF appears to be the main determinant of the lipopolysaccharide levels, clinical presentation, and outcome.

PCR-based calibration curves for studies of quantitative gene expression in human monocytes: development and evaluation.

BACKGROUND: Quantitative reverse transcription-PCR (RT-PCR) used to detect small changes in specific mRNA concentrations is often associated with poor reproducibility. Thus, there is a need for stringent quality control in each step of the protocol. METHODS: Real-time PCR-based calibration curves for a target gene, tissue factor (TF), and a reference gene, beta-actin, generated from PCR amplicons were evaluated by running cDNA controls. In addition, the reverse transcription step was evaluated by running mRNA controls. Amplification efficiencies of calibrators and targets were determined. Variances within and between runs were estimated, and power statistics were applied to determine the concentration differences that could reliably be detected. RESULTS: Within- and between-run variations (CVs) of cDNA controls (TF and beta-actin), extrapolated from reproducible calibration curves (CVs of slopes, 4.3% and 2.7%, respectively) were 4-10% (within) and 15-38% (between) using both daily and "grand mean" calibration curves. CVs for the beta-actin mRNA controls were 12% (within) and 19-28% (between). Estimates of each step's contribution to the total variation were as follows: CV(RT-PCR), 28%; CV(PCR), 15%; CV(RT), 23% (difference between CV(RT-PCR) and CV(PCR)). PCR efficiencies were as follows: beta-actin calibrator/target, 1.96/1.95; TF calibrator/target, 1.95/1.93. Duplicate measurements could detect a twofold concentration difference (power, 0.8). CONCLUSIONS: Daily PCR calibration curves generated from PCR amplicons were reproducible, allowing the use of a grand mean calibration curve. The reverse transcription step contributes the most to the total variation. By determining a system's total variance, power analysis may be used to disclose differences that can be reliably detected at a specified power.