Real-time Polymerase Chain Reaction Methodology Research Articles

Aberrant AML1 gene expression in the diagnosis of childhood leukemias not characterized by AML1-involved cytogenetic abnormalities.

The AML1 ( acute myeloid leukemia 1) gene, a necessary prerequisite of embryonic hematopoiesis and a critical regulator of normal hematopoietic development, is one of the most frequently mutated genes in human leukemia, involving over 50 chromosome translocations and over 20 partner genes. In the few existing studies investigating AML1 gene expression in childhood leukemias, aberrant upregulation seems to specifically associate with AML1 translocations and amplifications. The aim of this study was to determine whether overexpression also extends to other leukemic subtypes than the ones karyotypically involving AML1. We use quantitative real-time polymerase chain reaction methodology to investigate gene expression in 100 children with acute leukemias and compare them to those of healthy controls. We show that in childhood acute lymphoblastic leukemia, AML1 gene overexpression is associated with a variety of leukemic subtypes, both immunophenotypically and cytogenetically. Statistically significantly higher transcripts of the gene were detected in the acute lymphoblastic leukemia group as compared to the acute myeloid leukemia group, where AML1 overexpression appeared to associate with cytogenetic abnormalities additional to those that engage the AML1 gene, or that are reported as showing a "normal" karyotype. Collectively, our study shows that AML1 gene overexpression characterizes a broader range of leukemic subtypes than previously thought, including various maturation stages of B-cell acute lymphoblastic leukemia and cytogenetic types additional to those involving the AML1 gene.

Market Analysis of Food and Feed Products for Detection of Horse DNA by a TaqMan Real-Time PCR

Food-labelling regulations require that meat species in food and feed are accurately declared to the consumer. Traceability systems based on species identification through DNA analysis are potent tools for the supervision of food adulteration. In this study, a TaqMan real-time polymerase chain reaction (PCR) assay targeting a short mitochondrial 12S ribosomal RNA (rRNA) gene fragment of 73 base pair (bp) was developed for detection of horse DNA in different commercial meat products for human and pet consumption. The method was found to be specific for horse and did not show any cross-reactivity with different species of mammals, birds, fish and plants. The assay complies with the acceptance criteria required for real-time PCR methods in terms of applicability, linear dynamic range, accuracy and PCR efficiency and showed to be sensitive allowing the detection of 1 pg of horse DNA. A range of food and feed products (n = 171) was screened with the horse-specific real-time PCR to determine whether a correct labelling had been employed at the market level. Results obtained when testing the meat products for human consumption were in agreement with the labelling description provided by the suppliers. In the case of the pet foods, undeclared horse meat was detected in 21 % of the samples at low levels, suggesting unintentional cross-contamination during processing. The reported real-time PCR methodology may represent a suitable tool for the detection of food mislabelling.

L-DOPA Decarboxylase (DDC) Expression Status as a Novel Molecular Tumor Marker for Diagnostic and Prognostic Purposes in Laryngeal Cancer

l-DOPA decarboxylase (DDC) plays an essential role in the enzymatic synthesis of dopamine and alterations in its gene expression have been reported in several malignancies. Our objective was to analyze DDC messenger RNA (mRNA) and protein expression in laryngeal tissues and to evaluate the clinical implication of this molecule in laryngeal cancer. In this study, total RNA was isolated from 157 tissue samples surgically removed from 100 laryngeal cancer patients. A highly sensitive real-time polymerase chain reaction methodology based on SYBR Green I fluorescent dye was developed for the quantification of DDC mRNA levels. In addition, Western blot analysis was performed for the detection of DDC protein. DDC mRNA expression was revealed to be significantly downregulated in primary laryngeal cancer samples compared with their nonmalignant counterparts (P = .001). A significant negative association was also disclosed between DDC mRNA levels and TNM staging (P = .034). Univariate analysis showed that patients bearing DDC-positive tumors had a significantly decreased risk of death (hazard ratio = 0.23, P = .012) and local recurrence (hazard ratio = 0.32, P =.006), whereas DDC expression retained its favorable prognostic significance in the multivariate analysis. Kaplan-Meier curves further demonstrated that DDC-positive patients experienced longer overall and disease-free survival periods (P = .006 and P = .004, respectively). Moreover, DDC protein was detected in both neoplastic and noncancerous tissues. Therefore, our results suggest that DDC expression status could qualify as a promising biomarker for the future clinical management of laryngeal cancer patients.

L‐dopa decarboxylase (DDC) gene expression is related to outcome in patients with prostate cancer

What's known on the subject? and What does the study add? L-dopa decarboxylase (DDC) has been documented as a novel co-activator of androgen receptor transcriptional activity. Recently, it was shown that DDC gene expression is significantly higher in patients with PCa than in those with BPH. In the present study, there was a significant association between the DDC gene expression levels and the pathological stage and Gleason score of patients with prostate cancer (PCa). Moreover, DDC expression was shown to be an unfavourable prognostic marker of biochemical recurrence and disease-free survival in patients with PCa treated by radical prostatectomy. To determine whether L-dopa decarboxylase gene (DDC) expression levels in patients with prostate cancer (PCa) correlate to biochemical recurrence and disease prognosis after radical prostatectomy (RP). The present study consisted of 56 samples with confirmed malignancy from patients with PCa who had undergone RP at a single tertiary academic centre. Total RNA was isolated from tissue specimens and a SYBR Green fluorescence-based quantitative real-time polymerase chain reaction methodology was developed for the determination of DDC mRNA expression levels of the tested tissues. Follow-up time ranged between 1.0 and 62.0 months (mean ± SE, 28.6 ± 2.1 month; median, 31.5 months). Time to biochemical recurrence was defined as the interval between the surgery and the measurement of two consecutive values of prostate-specific antigen (PSA) ≥0.2 ng/mL. DDC expression levels were found to be positively correlated with the tumour-node-metastasis stage (P = 0.021) and Gleason score (P = 0.036) of the patients with PCa. Patients with PCa with raised DDC expression levels run a significantly higher risk of biochemical recurrence after RP, as indicated by Cox proportional regression analysis (P = 0.021). Multivariate Cox proportional regression models revealed the preoperative PSA-, age- and digital rectal examination-independent prognostic value of DDC expression for the prediction of disease-free survival (DFS) among patients with PCa (P = 0.036). Kaplan-Meier survival analysis confirms the significantly shorter DFS after RP of PCa with higher DDC expression levels (P = 0.015). This is the first study indicating the potential of DDC expression as a novel prognostic biomarker in patients with PCa who have undergone RP. For further evaluation and clinical application of the findings of the present study, a direct analysis of mRNA and/or its protein expression level in preoperative biopsy, blood serum and urine should be conducted.

Identification of novel cumulus cell molecular markers predictive of oocyte competence: confirmation with pregnancy outcome

To identify molecular markers predictive of human embryo implantation. Prospective Cohort Cumulus cells from all retrieved oocytes (No = 49) of 6 IVF patients who were chosen in random were mechanically separated prior to fertilization and frozen in liquid nitrogen for future evaluation. We selected heat shock protein transcription factor (HSF1), mitochondrial transcription factor A (TFAM), endoplasmic reticulum oxidoreductin1(ERO1LA), peroxiredoxin6 (PRDX6), and enolase 1(eno1), as well as 2 housekeeping genes (GAPDH and 28S RNA) for this study. Quantitative real-time Polymerase chain reaction methodology using standard curve analysis was employed to quantify the relative gene expression level. Unpaired student's t-test was used for statistical analysis. A mean of 2 ± 1.2 embryos were transferred per patient. There were three clinical pregnancies (positive group), one biochemical and two negative pregnancies (negative group). As shown in the table, among the five markers tested, HSF1 and Enolase1 were found to be significantly over expressed only in the negative group.Tabled 1GroupGADPH28SRNATFAMPRDX6ERO1 LAHSF1Enolase 1Positive Mean ± SEM21.6 ± 10.855.8 ± 4.130.7 ± 0.2319.9 ± 12.53.2 ± 1.387.5 ± 4.5269.8 ± 35.35Negative Mean ± SEM70.1 ± 29.3120.2 ± 12.212.8 ± 1.3546.9 ± 17.4111.2 ± 5.0∗∗81.3 ± 38.2∗P=0.04; P=0.03283.5 ± 115.3∗ P=0.04; P=0.03 Open table in a new tab Because of limited information provided by morphological assessment of embryos, IVF programs choose to transfer several rather than a single embryo to increase the odds of pregnancy. The unfortunate consequence of this practice is higher multiple pregnancy rates. Our study demonstrates a significant down regulation in the expression of HSF1 and enolase 1 in the cumulus cells of the oocytes that resulted in pregnancy. We conclude that low cumulus expression of HSF1 (playing a role in environmental and pathophysiological stresses) and Enolase1 (an enzyme of the glycolytic energetic pathway) may prove useful in selection of embryos most suitable for transfer.

The Novel Member of the BCL2 Gene Family, BCL2L12, Is Substantially Elevated in Chronic Lymphocytic Leukemia Patients, Supporting Its Value As a Significant Biomarker

BCL2L12 is a recently identified gene belonging to the BCL2 family, members of which are implicated in hematologic malignancies, including chronic lymphocytic leukemia (CLL). The aim of this study was to analyze the mRNA expression of the novel apoptosis-related gene BCL2L12 in patients with CLL and to examine its prognostic and predictive value and potential clinical application as a novel molecular biomarker for CLL. For this purpose, total RNA was isolated from peripheral blood of 65 CLL patients and 23 healthy donors. An ultrasensitive quantitative real-time polymerase chain reaction methodology for BCL2L12 and BCL2 mRNA quantification was developed using SYBR Green chemistry. After preparing cDNA by reverse transcription, relative quantification analysis was performed using the comparative C(T) (2(-ΔΔCT)) method. Furthermore, analysis of IGHV mutational status, CD38 expression, and detection of early apoptosis by double staining with Annexin V-FITC and propidium iodide were performed. According to our findings, BCL2L12 mRNA expression is significantly higher in CLL patients than in healthy donors. Receiver operating characteristic analysis demonstrated that BCL2L12 expression had significant discriminatory value, distinguishing very efficiently CLL patients from the non-leukemic population. Moreover, BCL2L12 expression predicts the presence of CLL, as demonstrated by both univariate and multivariate logistic regression analyses. Finally, high BCL2L12 mRNA levels are associated with advanced clinical stage and predict shorter overall survival in CLL patients.

Fundamental study of the radiation monitoring system based on evaluation of DNA lesions

The biological dosemeter that measures biological responses to ionising radiation is useful for radiation protection. This paper presents the development and characterisation of a gamma ray irradiation dosimetry system based on real-time PCR (polymerase chain reaction) methodology. Real-time PCR is used to amplify and simultaneously quantify a targeted DNA molecule. If there are no limitations due to limiting substrates or reagents, at each extension step, the amount of DNA target is doubled, leading to exponential (geometric) amplification of the specific DNA fragment. The essential point of this assay is that DNA lesions caused by ionising radiation block DNA synthesis by DNA polymerase, resulting in a decrease in the amplification of a damaged DNA template compared with that of non-damaged DNA templates.

A multiplatform real-time polymerase chain reaction detection assay for Vibrio cholerae

We report a multiplatform real-time polymerase chain reaction methodology based on genes encoding for the regulatory toxR activator and enterotoxin A protein to determine enterotoxigenic Vibrio cholerae types from other vibrios. This assay, which was successfully validated on a collection of 87 bacterial strains, including 63 representatives of V. cholerae and 8 noncholera vibrios provides a rapid tool for detection and identification of cholera.

Epstein–Barr virus infection is not a characteristic feature of multiple sclerosis brain

Multiple sclerosis is an inflammatory demyelinating disease of the central nervous system (CNS) that is thought to be caused by a combination of genetic and environmental factors. To date, considerable evidence has associated Epstein-Barr virus (EBV) infection with disease development. However, it remains controversial whether EBV infects multiple sclerosis brain and contributes directly to CNS immunopathology. To assess whether EBV infection is a characteristic feature of multiple sclerosis brain, a large cohort of multiple sclerosis specimens containing white matter lesions (nine adult and three paediatric cases) with a heterogeneous B cell infiltrate and a second cohort of multiple sclerosis specimens (12 cases) that included B cell infiltration within the meninges and parenchymal B cell aggregates, were examined for EBV infection using multiple methodologies including in situ hybridization, immunohistochemistry and two independent real-time polymerase chain reaction (PCR) methodologies that detect genomic EBV or the abundant EBV encoded RNA (EBER) 1, respectively. We report that EBV could not be detected in any of the multiple sclerosis specimens containing white matter lesions by any of the methods employed, yet EBV was readily detectable in multiple Epstein-Barr virus-positive control tissues including several CNS lymphomas. Furthermore, EBV was not detected in our second cohort of multiple sclerosis specimens by in situ hybridization. However, our real-time PCR methodologies, which were capable of detecting very few EBV infected cells, detected EBV at low levels in only 2 of the 12 multiple sclerosis meningeal specimens examined. Our finding that CNS EBV infection was rare in multiple sclerosis brain indicates that EBV infection is unlikely to contribute directly to multiple sclerosis brain pathology in the vast majority of cases.

Association Between Involuntary Smoking and Salivary Markers Related to Periodontitis: A 2‐Year Longitudinal Study

Insufficient data exist regarding the longitudinal influence of involuntary smoking on periodontitis progression. This study examined the relationship between involuntary smoking and periodontitis progression and the effects of involuntary smoking on salivary inflammatory and microbiologic markers related to periodontitis. Participants were recruited during annual health checkups in 2003 and 2005. In 2005, 200 of 273 (73%) Japanese employees examined at baseline underwent periodontal measurements, including clinical attachment level (CAL) and probing depth (PD). Periodontitis progression was identified when a subject displayed one or more teeth with an increase > or = 2.0 mm in CAL and PD during the 2 years. Salivary marker levels, including cotinine, were determined by enzyme assay, including enzyme-linked immunosorbent assay. The proportions of six periodontal pathogens in saliva were assessed using real-time polymerase chain reaction methodology. Based on receiver-operating characteristic analysis, non-, involuntary, and active smokers were defined as subjects exhibiting salivary cotinine levels of 0, 1 to 7, and > or = 8 ng/ml, respectively. By simple logistic regression analysis, age, alcohol consumption, smoking, breakfast habits, and working hours were related to the risk for significant periodontitis progression. Multiple logistic regression analysis revealed significantly higher periodontitis odds ratios (OR) in involuntary (OR = 2.23; 95% confidence interval [CI]: 1.03 to 4.83) and active (OR = 2.27; 95% CI: 1.02 to 5.04) smokers relative to non-smokers following adjustment for covariates. Levels of salivary markers, including albumin, aspartate aminotransferase, and lactoferrin, were significantly elevated in involuntary smokers relative to non-smokers. In contrast, the percentages of periodontal pathogens did not differ between the smoking groups, with the exception of Prevotella nigrescens, which displayed significantly lower levels in involuntary smokers compared to non-smokers. Involuntary smoking increased the inflammatory response and was associated with a greater risk for periodontitis progression.

The influence of the Ataxia-Telangiectasia mutated G5557A polymorphism on cervical cancer development

Introduction: DNA double strand break (DSBs) is one of the most serious threats to the integrity of the eukaryotic genome. One key protein that responds rapidly to this threat is Ataxia-Telangiectasia Mutated (ATM) protein kinase. Integration of Human Papillomavirus (HPV) DNA into the host genome is recognized as an essential step for the cell transformation and cervical cancer development. The aim of this study was to analyse the role of the ATM G5557A polymorphism in cervical cancer development. Material and Methods: We developed a retrospective study considering 484 cervical specimens of women from the northern Region of Portugal, using a real-time polymerase chain reaction methodology (assay C__26487857_10). Statistical analysis was performed using SPSS software. Results: No statistically significant differences were found, regarding the influence of the G5557A polymorphism with cytological classification, the presence or absence of HPV16 or other oncogenic high-risk HPV types (p>0.050). However, the ATM 5557A allele was found to influence the age at which the progression from LSIL to high-grade or invasive cervical cancer occurs (43.0 vs 59.0 years old; p=0.001). Conclusion: Our study reveals, for the first time, that ATM 5557A allele may influence cellular transformation leading low-grade lesions to progress to high-grade or invasive cervical cancer.

Application of maternal plasma DNA analysis for noninvasive prenatal diagnosis of Hb E-β-thalassemia

To establish simple noninvasive prenatal diagnosis of common beta-thalassemia in Southeast Asia, we have evaluated the possibility of identifying the 3 most common beta-thalassemia genes [beta(E), beta(17A-T), and beta(41/42(-CTCC))] by analysis of fetal DNA in maternal plasma using combined conventional polymerase chain reaction (PCR) and real-time quantitative PCR. Maternal plasma was obtained from peripheral blood of Thai pregnant women collected during the first and second trimesters of gestation. DNA was prepared from 200 microL plasma using a QIAmp Blood Mini Kit. Identifications of the beta(E), beta(41/42(-CTTT)), and beta(17A-T) in plasma DNA were carried out using semi-nested (for beta(E)) and nested (for beta(41/42) and beta(17)) real-time allele-specific PCR methodologies, and the results were compared with those obtained on fetal tissue analysis with routine invasive procedure. Twenty-six fetal beta(E) genes were correctly identified by maternal plasma DNA analysis of 39 pregnant women investigated. The fetal beta(41/42) and beta(17) mutations were detectable in 6 of 12 and 4 of 9 maternal plasma specimens, respectively, which were in concordance with the results obtained by routine invasive procedure. The noninvasive prenatal diagnostic methods developed should potentially prove useful for detection of paternally inherited mutation and for providing the exclusion of pregnancies at risk for this common genetic disorder in the region.

Trophoblastic Oxidative Stress and the Release of Cell-Free Feto-Placental DNA

Considerable quantities of cell-free fetal DNA circulate in the maternal blood during human pregnancy, but the origin of the DNA remains uncertain. Circumstantial evidence suggests the placenta is the principal source, so we tested the hypothesis that release occurs from the syncytiotrophoblast after the induction of apoptotic changes. Villous explants from normal placentas delivered by elective caesarean section were cultured under normoxic conditions (10% oxygen) for up to 20 hours or exposed to hypoxia (0.5% oxygen) for 1 hour followed by reoxygenation. The concentration of beta-globin cell-free DNA in the supernatant, measured using real-time polymerase chain reaction methodology, was significantly increased at 20 hours after hypoxia-reoxygenation. Release was associated with increased apoptosis, confirmed by increased activation of caspase-3 on Western blotting, and immunolocalized to the syncytiotrophoblast; necrosis was also evidenced by release of lactate dehydrogenase. Both release of cell-free DNA and apoptosis could be significantly reduced by the addition of antioxidant vitamins C and E to the culture medium. This study provides the first evidence of a mechanistic and quantitative link between placental apoptosis/necrosis and release of cell-free DNA, hence confirming that maternal serum/plasma concen-trations of cell-free DNA may act as a biomarker of trophoblast well-being during pregnancy.

Real-Time Polymerase Chain Reaction-Based Approach for Quantification of the pat Gene in the T25 Zea mays Event

In Europe, a growing interest for reliable techniques for the quantification of genetically modified component(s) of food matrixes is arising from the need to comply with the European legislative framework on novel food products. Real-time polymerase chain reaction (PCR) is currently the most powerful technique for the quantification of specific nucleic acid sequences. Several real-time PCR methodologies based on different molecular principles have been developed for this purpose. The most frequently used approach in the field of genetically modified organism (GMO) quantification in food or feed samples is based on the 5'-3'-exonuclease activity of Taq DNA polymerase on specific degradation probes (TaqMan principle). A novel approach was developed for the establishment of a TaqMan quantification system assessing GMO contents around the 1% threshold stipulated under European Union (EU) legislation for the labeling of food products. The Zea mays T25 elite event was chosen as a model for the development of the novel GMO quantification approach. The most innovative aspect of the system is represented by the use of sequences cloned in plasmids as reference standards. In the field of GMO quantification, plasmids are an easy to use, cheap, and reliable alternative to Certified Reference Materials (CRMs), which are only available for a few of the GMOs authorized in Europe, have a relatively high production cost, and require further processing to be suitable for analysis. Strengths and weaknesses of the use of novel plasmid-based standards are addressed in detail. In addition, the quantification system was designed to avoid the use of a reference gene (e.g., a single copy, species-specific gene) as normalizer, i.e., to perform a GMO quantification based on an absolute instead of a relative measurement. In fact, experimental evidences show that the use of reference genes adds variability to the measurement system because a second independent real-time PCR-based measurement must be performed. Moreover, for some reference genes no sufficient information on copy number in and among genomes of different lines is available, making adequate quantification difficult. Once developed, the method was subsequently validated according to IUPAC and ISO 5725 guidelines. Thirteen laboratories from 8 EU countries participated in the trial. Eleven laboratories provided results complying with the predefined study requirements. Repeatability (RSDr) values ranged from 8.7 to 15.9%, with a mean value of 12%. Reproducibility (RSDR) values ranged from 16.3 to 25.5%, with a mean value of 21%. Following Codex Alimentarius Committee guidelines, both the limits of detection and quantitation were determined to be <0.1%.

Decrease of serotonin receptor 2C in schizophrenia brains identified by high-resolution mRNA expression analysis

Background RNA expression profiling can provide hints for the selection of candidate susceptibility genes, for formulation of hypotheses about the development of a disease, and/or for selection of candidate gene targets for novel drug development. We measured messenger RNA expression levels of 16 candidate genes in brain samples from 55 schizophrenia patients and 55 controls. This is the largest sample so far used to identify genes differentially expressed in schizophrenia brains. Methods We used a sensitive real-time polymerase chain reaction methodology and a novel statistical approach, including the development of a linear model of analysis of covariance type. Results We found two genes differentially expressed: monoamine oxidase B was significantly increased in schizophrenia brain ( p = .001), whereas one of the serotonin receptor genes, serotonin receptor 2C, was significantly decreased ( p = .001). Other genes, previously proposed to be differentially expressed in schizophrenia brain, were invariant in our analysis. Conclusions The differential expression of serotonin receptor 2C is particularly relevant for the development of new atypical antipsychotic drugs. The strategy presented here is useful to evaluate hypothesizes for the development of the disease proposed by other investigators.