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Results for “Reverse Transcriptase Polymerase Chain Reaction”

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PubMed2000

Limitations of the nested reverse transcriptase polymerase chain reaction on tyrosinase for the detection of malignant melanoma micrometastases in lymph nodes.

The specificity and sensitivity of the nested reverse transcriptase polymerase chain reaction (RT-PCR) on tyrosinase was studied, for the detection of micrometastases of malignant melanoma. The specificity was assessed in the blood of six healthy donors, four patients with non-melanoma cancers of which one patient was treated with granulocyte-colony stimulating factor. Lymph nodes of nine patients without malignant melanoma were tested and four cell lines of various other tumours. Six of the nine non-melanoma lymph nodes were positive in this assay. The sensitivity was tested in a spike experiment in vitro, using a melanoma cell line. The detection limit was ten melanoma cells per 10(7) peripheral blood lymphocytes.

Biomarkers, Tumor↗
PubMed1998

Specificity of reverse transcriptase polymerase chain reaction assays designed for the detection of circulating cancer cells is influenced by cytokines in vivo and in vitro.

Several reverse transcriptase polymerase chain reaction (RT-PCR) assays have been described for the detection of circulating tumour cells in blood and bone marrow. Target mRNA sequences for this purpose are the cytokeratins (CK) 19 and 20, the carcinoembryonic antigen (CEA), and the prostate-specific antigen messages. In this study, we investigated biological factors influencing the specificity of the CK19 and CEA RT-PCR assays. Bone marrow, granulocyte colony-stimulating factor (G-CSF)-mobilized blood stem cells and peripheral blood samples obtained from healthy volunteers (n = 15; CEA n = 7), from patients with epithelial (n = 29) and haematological (n = 23) cancer and from patients with chronic inflammatory diseases (n = 16) were examined. Neither CEA nor cytokeratin 19 messages could be amplified from bone marrow samples from healthy subjects and from patients with haematological malignancies. In contrast, specimens from patients with inflammatory diseases scored positive up to 60%. To investigate the influence of inflammation on target mRNA expression, haemopoietic cells were cultured with and without cytokine stimulation in vitro. CK19 messages could be easily detected in cultured marrow cells without further stimulation, CEA messages only after gamma-interferon (gamma-INF) stimulation. In contrast, G-CSF-mobilized peripheral blood stem cells were positive for CK19 messages only after stem cell factor (SCF) or interleukin stimulation. We conclude that transcription of so-called tissue-specific genes is inductible in haemopoietic tissues under certain conditions. These factors have to be considered in future applications of RT-PCR for the detection of minimal residual disease.

Abdominal Neoplasms↗
PubMed2004

Retrospective comparison of qualitative and quantitative reverse transcriptase polymerase chain reaction in diagnosing and monitoring the ALL1-AF4 fusion transcript in patients with acute lymphoblastic leukaemia.

We compared quantitative reverse transcriptase polymerase chain reaction (Q-RT-PCR) to qualitative RT-PCR in determining response to therapy and predicting clinical outcome in 18 retrospectively selected patients with ALL positive for the ALL1-AF4 fusion and with frozen RNA samples collected at diagnosis and during follow-up (96 samples analysed). The ALL1-AF4 junction was detected by qualitative RT-PCR in 18 patients and by Q-RT-PCR in 17 patients (one patient harboured the rare e10-e6 ALL1-AF4 junction, which falls outside of the primer and probe location designed for the Q-RT-PCR). In three of the 12 patients negative to qualitative RT-PCR after induction therapy, a small number of ALL1-AF4 copies was detected by Q-RT-PCR. Thus nine patients were negative and eight positive. Seven of the eight positive patients suffered a relapse, including two of the three patients positive to Q-RT-PCR yet negative to qualitative RT-PCR. Moreover, we found two (5%) discordant results among the 39 follow-up tests of the nine patients who converted to a negative qualitative-quantitative PCR status. The results suggest that qualitative RT-PCR is more appropriate for the routine diagnosis of this genetic alteration. However, Q-RT-PCR is more accurate in assessing the molecular response after induction treatment and could be more useful in clinical decision-making in ALL1-AF4-positive ALL patients.

Adolescent↗
PubMed2003

Prognostic significance of reverse transcriptase polymerase chain reaction for prostate-specific antigen in metastatic prostate cancer: a nested study within CALGB 9583.

PURPOSE: To determine whether reverse transcriptase polymerase chain reaction (RT-PCR) to detect circulating prostate-specific antigen (PSA)-positive cells is a prognostic factor for survival in hormone refractory prostate cancer and to validate the prognostic importance of this test in relation to other known prognostic factors. PATIENTS AND METHODS: A single centralized laboratory received and analyzed whole blood for RT-PCR for PSA for a subset of patients enrolled on two Cancer and Leukemia Group B (CALGB) randomized trials (CALGB 9583 and CALGB 9480). Using 9583, a prognostic model was developed and an independent data set (CALGB 9480) was used to validate the fitted model. RESULTS: Of 162 patients in 9583, 91 (56%) patients were negative for RT-PCR for PSA and 71 (44%) patients were positive. The median survival time was 21 months (95% confidence interval [CI], 18 to 27 months) for RT-PCR-negative patients compared with 11 months (95% CI, 8 to 15 months) for RT-PCR-positive patients (P < or =.001). In multivariable analysis, the hazard ratio (HR) for death was 1.7 (95% CI, 1.2 to 2.4; P =.006) for positive RT-PCR patients compared with negative RT-PCR patients. A fitted model that incorporated RT-PCR for PSA and other factors was used to classify patients from 9480 into one of two risk groups: low or high. We observed good agreement between the observed and predicted survival probabilities for the two risk groups. CONCLUSION: RT-PCR to detect PSA-positive circulating cells is confirmed to be a significant prognostic factor of survival in patients with hormone refractory prostate cancer. This model could be used to stratify patients in randomized phase III trials.

Aged↗
PubMed2005

Lack of prognostic importance of reverse-transcriptase polymerase chain reaction detection of circulating messenger RNA in patients with melanoma.

BACKGROUND: Molecular serologic markers for detecting early melanoma metastases have been described. The objective of this study was to determine whether reverse-transcriptase polymerase chain reaction detection of circulating tyrosinase messenger RNA (mRNA) can identify the presence of subclinical metastases and predict subsequent clinical recurrence in surgically treated melanoma patients who are at significant risk for relapse. METHODS: Preoperative peripheral blood samples of disease-free melanoma patients, disease stage ranging from I to IV, were analyzed for the presence of tyrosinase mRNA by semiquantitative reverse-transcriptase polymerase chain reaction as a putative marker for circulating melanoma cells. Multivariate analysis was performed to evaluate the prognostic value of tyrosinase mRNA in the blood and in the correlating pathologic stage of disease with recurrence and survival. RESULTS: The study group consisted of 96 patients. The mean age was 54 years (range, 24 to 83 years). The mean Breslow thickness was 3 mm (range, 0.9 to 21 mm). Circulating melanoma cells were detected in 66 patients (69 percent). Blood polymerase chain reaction positivity by American Joint Committee on Cancer stage was as follows: stage I, 19 of 28 patients (68 percent); stage II, 17 of 25 patients (68 percent); stage III, 28 of 41 patients (68 percent); and stage IV, two of two patients (100 percent). Tyrosinase detection was not associated with stage of disease (p = 0.77). At a median follow-up of 30 months, disease recurred in 21 patients (22 percent), and 15 patients (16 percent) died. Disease stage of the patients correlated with recurrence (p < 0.0001) and death (p < 0.0001). The finding of mRNA tyrosinase in peripheral blood samples was not associated with recurrence (p = 0.1) or death (p = 0.77). CONCLUSIONS: The use of polymerase chain reaction to detect circulating tyrosinase mRNA in peripheral blood does not correlate with traditional prognostic indicators in patients with cutaneous melanoma and does not appear to be an effective prognostic tool.

Adult↗
PubMed1997

Quantitative reverse transcriptase polymerase chain reaction for measuring the N-methylpurine-DNA glycosylase mRNA level in rodent cells.

A modified quantitative reverse transcriptase polymerase chain reaction (QRT-PCR) procedure was developed for measuring mRNA concentration, in rodent cells, of the N-methylpurine-DNA glycosylase (MPG), a ubiquitous DNA repair protein responsible for the removal of N-alkylpurines and ethenoadducts of adenine, guanine, and cytosine from DNA. The method, applicable for quantitation of any mRNA, is based on the standard approach of comparing the relative amounts of PCR products of the experimental mRNA and a known amount of an exogenous reference RNA which is nearly identical to the experimental RNA. However, unlike in the earlier procedures in which deletion or insertion sequences were added to the reference RNA template, which may affect the efficiency of PCR but are needed to generate different size PCR products, experimental and reference RNAs yield PCR products of the same size in the new method. However, prior digestion with EcoRI allows separation of the two products because a unique EcoRI site was created in the reference RNA vector by point mutations. The QRT-PCR procedure is particularly useful for studying expression of the MPG gene whose mRNA level is very low and difficult to quantitate by Northern blot analysis. The number of MPG mRNA molecules/cell in late log-phase cultures varied from about 6 to 30 in several rodent lines. The SSV-NRK rat cell line has 6 +/- 0. 2 molecules/cell, while mouse NIH3T3 cells have about 30 +/- 1 molecules/cell. If the mRNA level is indicative of the level of the active MPG enzyme, these results may imply a variation in the capacity of various lines to remove the cytotoxic and mutagenic adducts from DNA.

3T3 Cells↗
PubMed1997

Detection of cytokine mRNA in unfractionated peripheral blood by reverse transcriptase polymerase chain reaction.

OBJECTIVE: To detect cytokine gene expression in unfractionated peripheral blood by reverse transcriptase-polymerase chain reaction (RT-PCR). DESIGN: Prospective study. SETTING: University hospital, Japan. SUBJECTS: 3 healthy volunteers and 3 severely infected patients. INTERVENTIONS: Peripheral blood was obtained and total RNA was extracted from 0.5 ml unfractionated whole blood with a 4 M guanidinium isothiocyanate mixture, 0.2 M sodium acetate, phenol, and chloroform. The mRNA was reverse transcripted, and interleukin-1 beta (IL-1beta) and tumour necrosis factor (TNF) cDNA were selectively amplified by synthetic primers with PCR. MAIN OUTCOME MEASURES: Establishment of cytokine gene expression in unfractionated peripheral blood. RESULTS: About 10 microg of total RNA was obtained from a 0.5 ml sample of blood. IL-1beta and TNF mRNA were not detected in blood from healthy volunteers, though they were detected in patients with severe infection. CONCLUSION: This method avoids artefactual gene activation and may be applicable to monitoring cytokine gene expression in various pathophysiological states.

Adult↗
PubMed1995

Detection of cytokine transcriptional profiles from bovine peripheral blood mononuclear cells and CD4+ lymphocytes by reverse transcriptase polymerase chain reaction.

Cytokine transcriptional profiles constitute important information about T cell mediated immunity against pathogens. We have developed a reverse transcriptase polymerase chain reaction (RT-PCR) assay to monitor gene expression of bovine T lymphocyte cytokines. Bovine cDNA was reverse transcribed from total RNA and subsequently amplified using primers designed from bovine or murine and human consensus sequences. Cytokine transcription of beta-actin, interleukins (IL) IL-1 alpha, IL-1 beta, IL-2, IL-4, IL-6, IL-10, tumor necrosis factor (TNF)alpha, TNF beta and interferon-gamma was detected from concanavalin A activated peripheral blood mononuclear cells and CD4+ purified T lymphocytes. The assay allows detection of many cytokine mRNA in a species where research has been hindered by lack of commercially available reagents and sequence information. RT-PCR analysis of lymphocyte cytokines will be invaluable for understanding the progression or resolution of disease as a consequence of lymphocyte response to specific antigens.

Animals↗
PubMed2001

Prognostic value of tyrosinase reverse-transcriptase polymerase chain reaction in metastatic melanoma.

BACKGROUND: Circulating tumor cells can now be identified in subjects with metastatic melanoma by using the reverse-transcriptase polymerase chain reaction (RT-PCR) to detect the messenger RNA of tyrosinase, a key enzyme of melanogenesis. AIM AND METHODS: The aim of this study was to determine whether the detection of positive tyrosinase cells in patients at metastatic stage was associated with a worse evolution. 32 patients were included with metastatic melanoma (AJCC IV). RESULTS: 66% had a positive tyrosinase RT-PCR and a shorter survival compared with patients with a negative RT-PCR, but this difference is not statistically significant. However, a positive test could appear indicative of rapid progression and poor prognosis. CONCLUSION: The prognostic value of this method could be improved by combining it with PCR of other melanoma markers (Melan A, Mage 3) or assays of serum markers (S 100 protein or lactate dehydrogenase).

Humans↗
PubMed2004

Semiquantitative determination of Alicyclobacillus acidoterrestris in orange juice by reverse-transcriptase polymerase chain reaction and capillary electrophoresis--laser induced fluorescence using microchip technology.

The semiquantitative detection of Alicyclobacillus acidoterrrestris in orange juice by reverse-transcriptase polymerase chain reaction (RT-PCR) with a linear dynamic range of 2 x 10(5)-2 colony forming units (CFU)/mL in terms of cell count is described. Separation, detection, and quantification of the RT-PCR products were accomplished using the Agilent 2100 bioanalyzer in conjunction with the DNA 1000 LabChip kit. After 0 and 12 h of enrichment, it was possible to generate a linear standard curve between the amount of cells and amplicon concentration of RT-PCR and PCR products. Using this method, cell diminution was verified in samples of orange juice treated with a natural inhibitor (Sapindus saponaria), determining the persistence of viable cells. Semiquantitative RT-PCR using the Agilent 2100 bioanalyzer is a potentially useful approach for rapid in vitro determination of A. acidoterrestris and monitoring of inhibitor susceptibility for the orange juice-producing industry.

Bacillus↗
PubMed2001

Prognostic significance of reverse transcriptase polymerase chain reaction for prostate-specific antigen in men with hormone-refractory prostate cancer.

PURPOSE: To evaluate the prognostic significance of reverse transcriptase polymerase chain reaction (RT-PCR) detection of prostate-specific antigen (PSA) mRNA in the blood of men with hormone-refractory prostate cancer (HRPC). PATIENTS AND METHODS: Peripheral blood was obtained from 193 men enrolled on Cancer and Leukemia Group B Study 9480, a prospective randomized comparison of three doses of suramin. RNA was isolated from the samples and assayed for the presence of PSA transcripts by RT-PCR. RESULTS: RNA could be isolated in 156 (83%) of samples. PSA transcripts as measured by RT-PCR were detectable in 75 (48%) of the 156 patients. The median survival for those patients in whom no transcripts were detectable was 18 months (95% confidence interval [CI], 14 to 22 months) compared with 13 months (95% CI, 11 to 15 months) (P =.004) for those in whom transcripts were detectable. In a multivariate analysis in which other factors predictive of survival were used, RT-PCR for PSA provided independent prognostic information. CONCLUSION: RT-PCR for PSA predicts survival duration in a population of men with HRPC.

Adenocarcinoma↗
PubMed2004

Quantification of melanoma mRNA markers in sentinel nodes: pre-clinical evaluation of a single-step real-time reverse transcriptase-polymerase chain reaction assay.

Although reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of melanocyte-associated mRNA can detect sentinel node melanoma metastases, most published assays are semi-quantitative methods of unknown sensitivity and precision, unsuitable for clinical use. We describe a single-step real-time quantitative RT-PCR assay for MART-1 and tyrosinase mRNAs, suitable for sentinel node analysis in a clinical setting. Using serial dilutions of melanoma cell line SK-MEL-28 RNA in water as a calibrator, we obtained linear calibration curves covering the range 0.5 to 10,000 arbitrary units (SK-MEL-28 melanoma cell equivalents). The sensitivity limit was 0.32 (MART-1) and 5 (tyrosinase) arbitrary units. Analytical imprecision was between 11% and 34%. MART-1 PCR efficiency was unaffected when samples were diluted with negative lymph node RNA rather than water, whereas tyrosinase PCR efficiency was halved. To evaluate the clinical suitability of our assay, we quantified melanocyte mRNAs in sentinel nodes with histologically verified micrometastases (n = 10) and benign nevus inclusions (n = 10), and in sentinel nodes without evidence of intranodal melanocytes (n = 10). We found significant differences in median melanocyte-derived mRNA levels comparing the three types of lymph nodes, suggesting that this quantitative molecular protocol may increase assay precision and be useful for the clinical evaluation of sentinel nodes.

Antigens, Neoplasm↗
PubMed2006

Prognostic significance of disseminated tumor cells as detected by quantitative real-time reverse-transcriptase polymerase chain reaction in patients with breast cancer.

BACKGROUND: In this study we have validated the feasibility of detecting disseminated tumor cells (DTC) by real-time reverse-transcriptase polymerase chain reaction (RT-PCR) analysis. Bone marrow samples from a large cohort of patients with breast cancer were analyzed for the presence of DTC by immunocytochemistry (ICC) or a molecular-based method. PATIENTS AND METHODS: Bone marrow samples were collected from 170 patients with breast cancer with stage I-IV disease before the initiation of any local or systemic treatment. Staining for cytokeratin (CK)-positive cells was performed with the Epimet kit. Disseminated tumor cells were also quantified by measuring relative gene expression for CK19 and mammaglobin (MAM) using a quantitative RT-PCR detection method. The mean follow-up time was 30 months. Kaplan-Meier analysis was used for predicting overall survival. RESULTS: Despite an excellent quantitative correlation and qualitative concordance between ICC and RT-PCR, survival analysis suggested an improved prognostic significance of DTC as detected by quantitative RT-PCR. Univariate survival analysis computed a relative risk of death of 2.87 for women with ICC-positive cells in the bone marrow, as compared with those without positive cells. The relative risk for women with RT-PCR-positive bone marrow was even higher: 3.5 (CK19) and 3.39 (MAM). In multivariate analysis, bone marrow CK19 was a stronger prognostic factor than bone marrow ICC. CONCLUSION: Reverse-transcriptase polymerase chain reaction-detected DTC is shown to be prognostically significant in untreated patients with breast cancer. Furthermore, it seems to be a more sensitive method for detecting DTC in bone marrow samples when compared with ICC.

Adult↗
PubMedDate not supplied

Evaluation of a p30 gene-based real-time reverse transcriptase polymerase chain reaction assay for detection of feline caliciviruses.

This report describes a feline calicivirus (FCV) p30 gene-based real-time SYBR Green I reverse transcriptase polymerase chain reaction (RT-PCR) assay that is capable of detecting low virus concentrations and a broad range of FCV isolates. The assay consisted of a 1-step RT-PCR reaction with primers delineating a 126-base-pair (bp) region of the FCV p30 gene. Sensitivity of the RT-PCR assay was determined to be equivalent to a FCV titer of 1.2 x 10(1) to 1.2 x 10(2) TCID50/mL. The assay was linear over a wide range of template concentrations and had a reaction efficiency of 95%. Specific FCV amplification products were detected from 51 wild-type FCV isolates, whereas specific products were not detected from a canine calicivirus, a rabbit calicivirus, and a bovine calicivirus. The primers used in this study amplified a large number of North American FCV isolates and further confirm the diagnostic utility of p30 gene-based real-time RT-PCR for detection of FCV.

Animals↗
PubMed1997

Quantification of MyoD, myogenin, MRF4 and Id-1 by reverse-transcriptase polymerase chain reaction in rat muscles--effects of hypothyroidism and chronic low-frequency stimulation.

A highly sensitive method of reverse-transcriptase polymerase chain reaction (RT-PCR) was established to quantify transcript levels of the myogenic regulatory factors MyoD, myogenin and MRF4 (muscle regulatory factor 4) and for Id-1 (inhibitor of differentiation), a putative negative regulator of myogenesis. The method was sensitive enough to detect mRNA amounts as low as 20 molecules. Measurements in 10 different skeletal muscles of the rat revealed that the amounts of the four factors differ by almost three orders of magnitude. Id-1 is expressed at lowest levels (approximately 4x10(5) molecules/microg RNA) and MRF4 at highest levels (approximately 9x10(7) molecules/microg RNA). In general, myogenin and MyoD mRNAs were inversely distributed in slow and fast muscles. A correlation seemed to exist between the levels of MyoD and myosin heavy chain (MHC) IIb, the fastest MHC isoform. However, as revealed by changes in the expression levels of these two regulatory factors under conditions of hypothyroidism and chronic low-frequency stimulation (CLFS), MyoD and myogenin did not seem to be strictly correlated with fast and slow myosins, respectively. Hypothyroidism led to pronounced depressions of MyoD, but only to small increases in myogenin mRNA in fast muscles. These changes were only slightly increased by CLFS. However, as previously shown, CLFS in combination with hypothyroidism induces in rat muscle pronounced fast to slow transitions in myosin expression [Kirschbaum, B. J., Kucher. H.-B., Termin, A., Kelly, A. M. & Pette, D. (1990) J. Biol. Chem. 265, 13974-13980]. These findings suggest that MyoD and myogenin may not be causally related to the development and maintenance of fiber-type diversities.

Animals↗
PubMed1993

Prospective application of reverse transcriptase polymerase chain reaction for diagnosing influenza infections in respiratory samples from a children's hospital.

A prospective clinical evaluation of the reverse transcriptase polymerase chain reaction (RNA PCR) for detection of influenza viruses was carried out with specimens from 342 patients of a children's hospital in The Netherlands. The RNA PCR, carried out directly on the specimens without an organic extraction, showed a sensitivity and specificity which are superior to those of direct immunofluorescence and comparable to those of cell culture combined with immunofluorescence (culture/IF). Negative results can be obtained within 2 days by the RNA PCR but may take up to 14 days by culture/IF. Because culturing is the standard technique for the detection of respiratory viruses, at this moment there are no strong arguments to replace culture/IF with RNA PCR for the detection of influenza A virus.

Base Sequence↗
PubMed1997

Bluetongue virus detection: a safer reverse-transcriptase polymerase chain reaction for prediction of viremia in sheep.

A reversible target capture viral RNA extraction procedure was combined with a reverse-transcriptase nested polymerase chain reaction (PCR) to develop a capture PCR assay providing a rapid and safe prediction method for circulating bluetongue virus in infected ruminants. This new assay was compared with virus isolation and a recently developed antigen-capture enzyme-linked immunosorbent assay (ELISA) for the detection of bluetongue virus. Eight Warhill crossbred sheep were inoculated subcutaneously with bluetongue virus serotype 10, and blood samples were taken sequentially over a period of 28 days. The capture PCR detected the peak of viremia, as determined by virus isolation and antigen-capture ELISA, from day 5 to day 14 after challenge. The results indicate that the rapid-capture bluetongue virus PCR provides a rapid indicator of samples in which virus can be isolated. In addition, this capture bluetongue virus PCR procedure does not require a lengthy phenol extraction or the use of the highly toxic methyl mercury hydroxide denaturant.

Animals↗
PubMed2005

Use of real-time reverse transcriptase polymerase chain reaction assay and cell culture methods for detection of swine influenza A viruses.

OBJECTIVE: To evaluate sensitivity and specificity of a real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay performed on pooled nasal swab specimens, compared with virus isolation performed on individual nasal swab specimens by use of 2 cell culture lines for detection of swine influenza A viruses. SAMPLE POPULATION: 900 nasal swab specimens obtained from pigs at an abattoir and 62 nasal swab specimens submitted for diagnostic testing. PROCEDURES: Primers were chosen to amplify a conserved portion of the influenza virus matrix gene. Assay sensitivity was initially determined by testing serial dilutions of various subtypes of swine influenza viruses. Sensitivity and specificity were confirmed by use of nasal swab specimens with or without addition of known concentrations of influenza virus and further validated by testing nasal swab specimens obtained through an abattoir surveillance program or submitted for diagnostic testing. Aliquots of specimens were pooled in sets of 10, and results of real-time RT-PCR assays were compared with results of virus isolation of individual specimens in Madin Darby canine kidney (MDCK) and mink lung (Mv1Lu) cells. RESULTS: Real-time RT-PCR assay was highly specific (100%) and sensitive (88% to 100%). Among the 16 viruses isolated, 3 grew only in Mv1Lu cells and 3 grew only in MDCK cells. CONCLUSIONS AND CLINICAL RELEVANCE: Results indicate that real-time RT-PCR assay is a fast and accurate test for screening numerous nasal swab specimens for swine influenza virus. Some viruses were isolated in only MDCK or Mv1Lu cells, indicating that use of >1 cell line may be required to isolate a broad range of influenza A viruses.

Animals↗