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Results for “Reverse Transcriptase Polymerase Chain Reaction”

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At least 307 records · Page 17Linked to original sources
PubMed1996

Rapid detection of thymidylate synthase gene expression levels by semi-quantitative competitive reverse transcriptase polymerase chain reaction followed by quantitative digital image analysis.

We describe a simplified and reliable polymerase chain reaction (PCR) method to quantify thymidylate synthase (TS) gene expression levels from clinical human tumor biopsy samples as small as 100 mg using the beta-actin housekeeping gene as a reference standard. The semiquantitative RT-PCR is carried out by the coamplification of the target template and an external competitor using primer pairs common to both templates in the same reaction vessel. Quantitative digital image analysis is performed directly after electrophoresis, thus mRNA quantification is done quickly and without the use of radioactive substances. The observed relative TS gene expression levels varied between 3- and 40-fold, but most of the values were grouped within a 10-fold range. There is an observed 89% correlation between TS mRNA expression and protein levels. These findings suggest that preliminary experiments used to determine the linear range of RT-PCR amplification in non-competitive semiquantitative PCR experiments, and the use of radioactive substances to quantify PCR products may be unnecessary.

Base Sequence↗
PubMed1999

Molecular pathology of leukemia and lymphoma.

Molecular dissection of physiologic and pathologic genetic phenomena in hematologic malignancy has provided the pathologist with a broad menu of new assays. By integrating the data gleaned from these techniques we can formulate more rational and biologically based diagnoses, which should lead to the ultimate goal of targeted therapy for these specific entities. We summarize some of the more relevant molecular genetic assays and present an overview of those genetic mechanisms usually evaluated in the current practice of hematopathology. The usefulness of such assays extends beyond refining diagnoses in that they also provide relevant prognostic information. Moreover, since most are based on the polymerase chain reaction and reverse transcriptase polymerase chain reaction, we are more sensitively able to monitor for residual disease after attempts at curative therapy, and our definition of remission has been dramatically altered. However, molecular genetic tests are not without limitations, and we must remain cognizant of their cost effectiveness and be aware of current deficiencies in standardization. The challenge will be to meaningfully and economically harness and integrate the information we obtain from these and future technologies into appropriate clinical practice.

DNA, Neoplasm↗
PubMed2003

[A case report and pedigree study of a single point mutation in RET proto-oncogene and type 2B multiple endocrine neoplasia].

OBJECTIVE: To determine the relationship between a single point mutation in RET proto-oncogene and the occurrence of multiple endocrine neoplasia type 2B (MEN-2B) in a Chinese pedigree. METHODS: We used the methods of polymerase chain reaction (PCR), reverse transcriptase polymerase chain reaction (RT-PCR) and direct gene sequencing of PCR products by an automated DNA sequencer to scan the entire exon 16 of RET proto-oncogene in the tumor (c)DNA from one patient with MEN-2B and the leukocyte DNA from this patient and both of his parents. RESULTS: We found the same mutation Met(ATG)-->Thr(ACG) at codon 918 in exon 16 of RET proto-oncogene in both the tumor (c)DNA and leukocyte DNA of the MEN-2B patient in the form of homozygous missense mutation, but there was no corresponding mutation in leukocytes DNA of his parents. CONCLUSION: We propose that in Chinese population, the point mutation M918T is also associated with the onset of MEN-2B and this case of MEN-2B is sporadic. Thus it may provide a genetic basis for the early diagnosis and treatment of patients suffering from MEN-2B and their at-risk family members in Chinese population.

Adolescent↗
PubMed2003

[Detection of gene promoter methylation and mRNA, protein expression levels of E-cadherin in nasopharyngeal carcinoma].

OBJECTIVE: To detect the gene promoter methylation, mRNA and protein expression levels of E-cadherin and beta-catenin in primary and metastatic tumor samples of nasopharyngeal carcinoma (NPC), and to investigate the mechanism of invasion and metastasis of neoplastic cell in NPC. METHODS: Twenty-one patients with NPC were studied. The samples of primary tumor and paired lymph node metastatic tumor were collected and examined for aberrant gene promoter methylation in E-cadherin by DNA Methylation-specific polymerase chain reaction (MSP). Reverse transcriptase polymerase chain reaction (RT-PCR), Western blotting and immunohistochemical staining were adopted to detect mRNA and protein levels of E-cadherin and beta-catenin. RESULTS: (1) The gene promoter methylation in E-cadherin was 52.4% (11/21) in primary tumor of NPC, and 80.9% (17/21) in lymph node metastatic tumor, which existed significant difference (P < 0.05). (2) In primary tumor, about 80% (0 approximately 100%) neoplastic cells expressed E-cadherin protein on the average, which was significantly higher than that of metastatic tumor (50% on the average, P = 0.004). The expression levels of beta-catenin protein were high in both primary and metastatic tumors, but with no statistic difference (P = 0.698). (3) By Western blotting analysis, the relative intensity of protein expression in E-cadherin was significantly higher in primary tumor (206.7 +/- 32.7) compared to that of metastatic tumor (65.0 +/- 15.9), while the expression of beta-catenin protein showed no difference between them (P = 0.754). (4) mRNA expression level of E-cadherin was higher in primary tumor than that of metastatic tumor.No remarkable difference was found for the mRNA expression of beta-catenin. CONCLUSIONS: (1) Downregulation of mRNA and protein expression of E-cadherin may play a critical role in neoplastic cell invasion and metastasis in NPC. The aberrant promoter methylation of E-cadherin may ultimately alter the mobility and scattering of tumor cells in NPC. (2) Downregulation of E-cadherin alone may be enough for the tumor cell to lose intercellular adhesions which results in tumor cell invasion and metastasis. However, mutant beta-catenin could also involve in this progress. (3) The detection of gene promoter hypermethylation of E-cadherin should be evaluated in the screening and surveillance of NPC.

Adult↗
PubMed2004

Detection of melanoma cells in sentinel lymph nodes by reverse transcriptase-polymerase chain reaction: prognostic significance.

BACKGROUND: Recently reverse transcriptase-polymerase chain reaction (RT-PCR) has been proposed as a new sensitive method for the detection of submicroscopic melanoma nodal metastases. Sentinel lymph node (SLN) status is considered the most important prognostic factor for melanoma patients. Thus, in recent years, melanoma research has been focused on identifying new molecular markers of micrometastases. METHODS: In this study, 129 SLNs were collected and analyzed by RT-PCR for tyrosinase and melanoma inhibitory activity (MIA) messenger RNA (mRNA) expression. RESULTS from PCR analysis were then compared with those obtained by hematoxylin and eosin and immunohistochemistry and related to progression of disease. RESULTS: MIA gene expression was positive by RT-PCR in 27% of the tyrosinase-positive SLNs. When the correlation between tyrosinase and/or MIA mRNA expression and disease-free survival was evaluated by the Kaplan-Meier exact test, there was a statistically significant correlation between simultaneous tyrosinase and MIA gene expression in SLNs and progression of disease. CONCLUSIONS: RT-PCR analysis for both MIA and tyrosinase mRNA may identify a subset of melanoma patients with a worse prognosis whom the routine methods, such as histology and immunohistochemistry, fail to identify because of the poor sensitivity of these methods.

Disease-Free Survival↗
PubMed2005

Heat-treated Campylobacter spp. and mRNA stability as determined by reverse transcriptase-polymerase chain reaction.

The detection method of reverse transcriptase-polymerase chain reaction (RT-PCR), which specifically targets mRNA, was developed and tested for detection of cultivable Campylobacter spp. The expression of four DNA targets- flaA, tkt, porA, and a putative haem-copper oxidase domain-were assayed in heat-inactivated Campylobacter spp. to determine an optimum target for RT-PCR amplification. A diversity of Campylobacter spp. was tested; however, the presented RT-PCR technique was specific for C. jejuni, C. coli, and C. lari. The durability of mRNA species detected by our RT-PCR technique was dependent upon the individual Campylobacter spp. examined, the condition of heat treatment and post-treatment holding time, as well as the transcript targeted. The putative oxidase was determined to be the most stable mRNA species for this assay. The mRNA of the putative oxidase gene was detectable even after Campylobacter spp. had been treated at temperatures of 95-99 degrees C. Using DNA-based PCR, the four DNA targets could be amplified after heat inactivation followed by a 48 h holding time, indicating that the chromosomal DNA was not substantially degraded by the heat treatment. PCR products from the putative oxidase gene were detected at 10(2) to 10(3) C. jejuni CFU per mL, exhibiting the highest level of sensitivity among the genes tested. The results in the present study indicate that mRNA from Campylobacter spp. may persist in a form that is detectable by RT-PCR amplification for an extended period after heat treatment, demonstrating a poor correlation between mRNA detection and cell cultivability. With these results in mind, further investigations are necessary to determine the correlation between RT-PCR amplification and viability.

Bacterial Proteins↗
PubMed1992

Detection of Norwalk virus in stool specimens by reverse transcriptase-polymerase chain reaction and nonradioactive oligoprobes.

A reverse transcriptase (RT)-polymerase chain reaction (PCR)-oligoprobe (OP), or RT-PCR-OP, method was developed for the detection of the Norwalk virus, which causes acute, epidemic gastroenteritis, in stool specimens. The Norwalk virus genome regions encoding the following two proteins were amplified by RT-PCR: the RNA polymerase (260-bp product) and a putative immunogenic protein (224-bp product). The resulting DNA fragments (amplicons) were hybridized to a digoxigenin-labeled internal OP specific to each amplicon. The detection limit of Norwalk virus, as determined by the endpoint of RT-PCR amplification for serially diluted, positive stool specimens, was similar to the actual virion titer as estimated by electron microscopy and at least 100-fold greater than the titer determined by radioimmunoassay (RIA). The RT-PCR-OP assay was specific for Norwalk virus and negative for other enteric viruses, including human and animal caliciviruses, hepatitis E virus, Snow Mountain agent, astroviruses, 16 human enteroviruses, and 5 human rotaviruses. Components of fecal specimens that interfere with RT-PCR were removed successfully by Sephadex G-200 gel chromatography. Of 20 stool specimens from human volunteers that were positive for Norwalk virus by RIA, a specific RT-PCR-OP result was obtained in 95% (19 of 20) of the samples by using the immunogenic protein primers and 75% (15 of 20) by using the polymerase primers. Twenty-six stool specimens from asymptomatic children and adults were negative by the Norwalk virus RT-PCR-OP. RT-PCR-OP detected Norwalk virus in the 4 of 21 coded fecal specimens that were also positive by enzyme immunoassay. Two samples that were positive by RIA or enzyme immunoassay were negative by RT-PCR, perhaps because viral RNA was not present or RT-PCR inhibitors were not adequately removed.

Adult↗
PubMed2006

Specific detection of cytokeratin 20-positive cells in blood of colorectal and breast cancer patients by a high sensitivity real-time reverse transcriptase-polymerase chain reaction method.

A real-time reverse transcriptase-polymerase chain reaction (RT-PCR) method for detection of cytokeratin 20-positive cells in blood characterized by two novel features was developed and tested on 99 patients with colorectal cancer, 110 with breast cancer, and 150 healthy subjects. To optimize the specificity and sensitivity of the method, two novel features were used. First, a primer overlapping two adjacent exons was generated to inhibit nonspecific amplification both in healthy donors and cancer patients; second, a non-end-point first-round amplification was used to increase sensitivity. The number of first-round cycles was chosen to reach the highest level of sensitivity while conserving quantitative characteristics. PCR efficiency increased from 88.9% in single-round RT-PCR to 99.0% in nested real-time RT-PCR. To establish sensitivity and specificity of the method, HT29 cells were serially diluted with normal blood. Detection limit improved from 100 HT29 cells (single-round RT-PCR) to 1 to 10 cells (nested real-time RT-PCR) per 3 ml of whole blood. None of the healthy subjects was positive, whereas 22 and 29% of all colorectal and breast cancer patients, respectively, had cytokeratin 20 cell equivalents in blood. The association between cytokeratin 20 cell equivalents and metastasis was statistically significant for breast (P = 0.026) but not colorectal cancer patients (P = 0.361). Negativity of all 150 healthy controls examined confers diagnostic potential to the method.

Biomarkers, Tumor↗
PubMed1993

Quantitation of tropoelastin mRNA and assessment of alternative splicing in human skin fibroblasts by reverse transcriptase-polymerase chain reaction.

We have developed a reverse transcriptase-polymerase chain reaction (RT-PCR) assay for the quantitative measurement of levels of tropoelastin mRNA in total RNA preparations from skin fibroblasts. This method facilitates the reproducible detection of low abundance tropoelastin mRNA in the range of 10-1000 copies per cell. The procedure is based on a competitive RT-PCR assay where a tropoelastin cDNA-derived internal RNA standard is cotranscribed and coamplified together with the sample derived-endogenous target mRNA. In addition, RT-PCR of several domains of tropoelastin mRNA, followed by DNA sequence analysis of asymmetric PCR products, revealed a previously unknown pattern of alternate exon usage at the 3' end of the tropoelastin gene in human skin fibroblasts.

Alternative Splicing↗
PubMed1996

Short report: development of a new diagnostic method for Plasmodium falciparum infection using a reverse transcriptase-polymerase chain reaction.

We describe here a reverse transcriptase-polymerase chain reaction method for the detection of malaria parasites. Ten in vitro-cultured isolates of Plasmodium falciparum and 16 specimens from patients infected with P. falciparum were used to examine the specificity and sensitivity of the test. The sensitivity of the test was 0.3 parasites per microliter of blood. Specificity was determined by matching the sequences of the specimens' DNA to published sequences of 18S ribosomal RNA genes in the species-specific region. The test proved to be very sensitive and specific for the detection of P. falciparum infection.

Animals↗
PubMed2003

Search for phase specific genes in the brain of desert locust, Schistocerca gregaria (Orthoptera: Acrididae) by differential display polymerase chain reaction.

Differential display reverse transcriptase polymerase chain reaction (DDRT-PCR) in combination with semi-quantitative RT-PCR was used to compare differences in gene expression between the solitary and gregarious phase of Schistocerca gregaria. Twenty-six primer combinations were used, which produced 8 differential bands. Two out of the 8 differentials, one typical for the solitary and one for the gregarious phase, were further analyzed by semi-quantitative RT-PCR. The expression level of the solitary phase specific gene (SSG) was 2 times higher in solitary animals as compared to gregarious ones, while the gregarious specific gene (GSG) gave a 4-fold higher expression level in gregarious animals than in solitaries. Sequence analysis demonstrated that SSG does not belong to a known gene family, while the GSG belongs to the SPARC protein family.

Amino Acid Sequence↗
PubMedDate not supplied

Detection of tumor cells in peritoneal lavages from patients with gastrointestinal cancer by multiplex reverse transcriptase PCR.

BACKGROUND/AIMS: Cytological examination of peritoneal lavages is a useful predictor of peritoneal recurrence in gastrointestinal carcinoma patients. Nevertheless, it may be inadequate for those patients with lavages containing only few cancer cells. In the present study, sensitive detection of free cancer cells could be achieved through amplification of cytokeratin 19, carcinoembryonic antigen, alpha-fetoprotein mRNAs by means of multiplex reverse transcriptase polymerase chain reaction and nested polymerase chain reaction. METHODOLOGY: The multiplex reverse transcriptase polymerase chain reaction assay was used to examine lavage samples from 64 patients with various gastrointestinal malignant lesions (colorectal n = 27; duodenal carcinoma n = 1; gastric n = 7; pancreatic n = 4; hepatocellular carcinoma n = 2; gallbladder n = 1; cholangiocellular carcinoma n = 2 and 20 colorectal liver metastases. Specificity was assessed by examination of 15 donors without malignancies. In addition, nested polymerase chain reaction was used to improve the sensitivity of the assay for the detection of alpha-fetoprotein transcripts. RESULTS: Peritoneal lavages from 12 of 64 gastrointestinal carcinoma patients were positive for carcinoembryonic antigen mRNA. Carcinoembryonic antigen proved a specific marker, as no false-positives were detected in any patients without gastrointestinal cancer. alpha-fetoprotein mRNA was detected exclusively in peritoneal lavages from tumor patients, i.e., in 16 of 27 colon cancer patients, 14 of 20 patients with colorectal liver metastasis, 2 of 7 patients with gastric cancer, two patients with hepatocellular carcinoma and 2 of 4 patients with pancreatic cancer. Cytokeratin 19 mRNA was not found a useful marker, since control patients without malignancies were also positive. CONCLUSIONS: Our data suggest that carcinoembryonic antigen- and alpha-fetoprotein mRNA in peritoneal lavage are potentially useful specific markers for early diagnosis of metastasis of gastrointestinal cancer. It has been shown that alpha-fetoprotein-specific nested reverse transcriptase polymerase chain reaction can detect not only hepatocellular carcinoma cells, but also malignant cells from other gastrointestinal carcinomas. In contrast, cytokeratin 19 mRNA lacks specificity for gastrointestinal cancer.

Biomarkers, Tumor↗
PubMed2005

Reverse transcriptase-polymerase chain reaction to detect avian encephalomyelitis virus.

A reverse transcriptase-polymerase chain reaction (RT-PCR) was developed and optimized for the detection of avian encephalomyelitis virus (AEV). A pair of primers was prepared based on the VP2 gene of the structural protein P1 region of the AEV genome. An avian encephalomyelitis virus-specific 619-base pair cDNA product was amplified by these primers from five reference/field strains of AEVs but not from 10 other avian pathogenic viruses and bacteria. The RT-PCR assay developed in this study was found to be sensitive and specific with as little as 10 pg of avian encephalomyelitis virus RNA detected using gel electrophoresis. Furthermore, AEV-RT-PCR was able to detect AE virus from chicken embryo brain at 3 days postinoculation as compared with the AE agar gel precipitation test (AGP), which required up to 11 days of incubation in the embryos.

Animals↗
PubMed2004

Detection of infectious hepatitis A virus by integrated cell culture/strand-specific reverse transcriptase-polymerase chain reaction.

AIMS: A novel integrated cell culture/strand-specific reverse transcriptase-polymerase chain reaction (RT-PCR) assay was established for detection of infectious hepatitis A virus (HAV). METHODS AND RESULTS: The specificity of tagged RT-PCR was assessed using HAV genomic positive-strand RNA extracted from HAV virions as reference. Water samples artificially contaminated with infectious or formalin-inactivated HAV were subjected to integrated cell culture (ICC)/RT-PCR and ICC/strand-specific RT-PCR assays respectively. The tagged RT-PCR had high specificity for HAV negative-strand RNA. By demonstrating the formation of negative-strand RNA replicative intermediate, ICC/strand-specific RT-PCR can distinguish between infectious and non-infectious HAV. The described method detected infectious HAV at inoculation level of 10(0) TCID50 per flask within 4 days. CONCLUSIONS: The ICC/strand-specific RT-PCR is a novel, rapid, sensitive and reliable method for detection of infectious HAV. SIGNIFICANCE AND IMPACT OF THE STUDY: Coupled with a suitable virus concentration and purification system, ICC/strand-specific RT-PCR will provide a novel and rapid method for detection of infectious HAV in clinical, environmental and food samples. This assay may be used as an alternative method to test the effective inactivation of inactivated virus vaccines. It may also be adapted to assess the efficacy of disinfection of HAV and enteric viruses in foods and water.

Cell Line↗
PubMed1999

The detection of renal carcinoma cells in the peripheral blood with an enhanced reverse transcriptase-polymerase chain reaction assay for MN/CA9.

BACKGROUND: Using a reverse transcriptase-polymerase chain reaction (RT-PCR) assay, the authors previously determined the expression of MN/CA9 mRNA in renal cell carcinoma (RCC) and its absence in benign renal tissue. In the current study, the utility of an enhanced RT-PCR assay in the detection of renal carcinoma cells in the peripheral blood was assessed. METHODS: An enhanced MN/CA9 RT-PCR assay was applied to peripheral blood samples from a total of 96 patients. Forty-two patients had renal tumors, including 5 with benign renal lesions, 28 with localized RCC, and 9 with metastatic RCC. Fifty-four control patients without renal tumors were similarly tested. Pathologic staging for patients with localized cancer was T1N0M0 for 5, T2N0M0 for 9, and T3N0M0 for 14 patients. RESULTS: Cells expressing MN/CA9 were detected in 1 of 54 controls (1.8%) and in 18 of 37 cancer patients (49%). Thirteen of twenty eight patients (46%) with localized RCC and 5 of 9 (56%) with metastatic disease tested positive with the assay. No patient with a benign renal tumor exhibited MN/CA9 expression. All blood test results for patients with clear cell RCC were noted to be positive. No correlation was noted between MN/CA9 results and age, gender, or tumor grade. The differences in MN/CA9 results according to T classification were not statistically significant. CONCLUSIONS: The enhanced RT-PCR assay for MN/CA9 is a highly specific technique for detecting circulating renal carcinoma cells in the peripheral blood, and it may prove useful in the diagnosis and monitoring of RCC.

Adult↗