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PubMed2025

Quantitative Real-Time PCR for Circular RNA Detection and Analysis.

In eukaryotes, nearly 2% of the genome represented by the coding proteins. However, emerging evidence suggest more than 75% of the human genome referred to as noncoding part also plays a crucial role in governing major regulatory pathways. Noncoding RNAs can be categorized into several groups, such as microRNAs (miRNAs), small nuclear RNA (snRNAs), small nucleolar RNA (snoRNAs), transfer RNA (tRNA), and circular RNA (circRNAs), which contribute to this regulatory landscape. Circular RNAs (circRNAs) are identified as a new class of regulatory noncoding RNAs with gene regulatory roles by acting as miRNA or RNA binding protein sponges or interacting with proteins. Researchers employ quantitative real-time PCR methods to examine circular RNA expression utilizing divergent primers for identification and quantification.

RNA, Circular↗
PubMed1993

Renin messenger RNA, detected by polymerase chain reaction, can be switched on in rat atrium.

OBJECTIVE: The aim of the present study was to use a highly sensitive, polymerase chain reaction (PCR) technique to examine the controversial question of renin gene expression in the heart and to determine whether expression in cardiac tissue can be stimulated. DESIGN: The study involved female Wistar rats fed either a normal-sodium diet or a low-sodium diet, together with an angiotensin I converting enzyme inhibitor, enalapril, orally for 1 week. METHODS: RNA was extracted from atrium, ventricle, kidney (positive control) and submandibular gland (negative control) and, after reverse transcription into complementary DNA, was used in a 35-cycle PCR. Reaction products were visualized after electrophoresis by ethidium bromide staining and hybridization probing with [32P]-labelled target oligonucleotide. RESULTS: Atrial RNA from sodium-replete rats gave little or no renin messenger (m)RNA PCR product on ethidium bromide-stained gels. After DNA transfer, followed by hybridization probing and extended autoradiography, a faint band was seen. In sharp contrast, atrial extracts from sodium-depleted enalapril-treated rats displayed a pronounced band of hybridization, corresponding in size to that expected for renin mRNA. No band was seen for ventricle. CONCLUSION: The present PCR study has shown that in the normal sodium-replete rat, atrial tissue has only very low renin gene expression, but that after a low-sodium diet + treatment with enalapril, expression is switched on in atrium. Ventricular tissue does not express the renin gene in either state.

Animals↗
PubMed1993

Human immunodeficiency virus type 1 RNA detection in peripheral blood mononuclear cells by polymerase chain reaction: enhanced sensitivity after mitogenic stimulation.

The aim of this study was to investigate whether stimulus-induced up-regulation of human immunodeficiency virus type 1 (HIV-1) expression in peripheral blood mononuclear cells (PBMC) could enhance the diagnostic sensitivity of the polymerase chain reaction (PCR). PBMC derived from 11 HIV-1-infected asymptomatic adults were cultured with a stimulus of phytohemagglutinin (PHA) plus phorbol 12-myristate 13-acetate (PMA) for 36 h prior to lysing the cells for PCR. In all 11 patients studied, the intensity of PCR-assisted HIV RNA amplification (RNA-PCR) performed on stimulated cells was significantly (p < 0.001) higher than that obtained on unstimulated cells. A comparison of conventional PCR-assisted DNA amplification (DNA-PCR) with that of RNA-PCR was made on seven patients. The sensitivity of DNA-PCR was also increased by prior stimulation of cells, although not to the same extent as was observed for RNA-PCR. The results of our study indicate that the sensitivity of PCR can be significantly enhanced by prior activation of cells with PHA and PMA.

Adult↗
PubMed2006

Development of a quantitative-competitive PCR for quantification of human cytomegalovirus load and comparison with antigenaemia, viraemia and pp67 RNA detection by nucleic acid sequence-based amplification.

AIM: The human cytomegalovirus (HCMV) is an important pathogen in immunocompromised patients, such as transplant recipients. The use of sensitive and rapid diagnostic assays can have a great impact on antiviral prophylaxis and therapy monitoring and diagnosing active disease. Quantification of HCMV DNA may additionally have prognostic value and guide routine management. The aim of this study was to develop a reliable internally-controlled quantitative-competitive PCR (QC-PCR) for the detection and quantification of HCMV DNA viral load in peripheral blood and compare it with other methods: the HCMV pp65 antigenaemia assay in leukocyte fraction, the HCMV viraemia, both routinely employed in our laboratory, and the nucleic acid sequence-based amplification (NASBA) for detection of HCMV pp67-mRNA. METHODS: Quantitative-competitive PCR is a procedure for nucleic acid quantification based on co-amplification of competitive templates, the target DNA and a competitor functioning as internal standard. In particular, a standard curve is generated by amplifying 10(2) to 10(5) copies of target pCMV-435 plasmid with 10(4) copies of competitor pCMV-C plasmid. Clinical samples derived from 40 kidney transplant patients were tested by spiking 10(4) copies of pCMV-C into the PCR mix as internal control, and comparing results with the standard curve. RESULTS: Of the 40 patients studied, 39 (97.5%) were positive for HCMV DNA by QC-PCR. While the correlation between the number of pp65-positive cells and the number of HCMV DNA genome copies/mL and the former and the pp67mRNA-positivity were statistically significant, there was no significant correlation between HCMV DNA viral load assayed by QC-PCR and HCMV viraemia. CONCLUSIONS: The QC-PCR assay could detect from 10(2) to over 10(7) copies of HCMV DNA with a range of linearity between 10(2) and 10(5) genomes.

Adult↗
PubMed1993

Alterations in spliced and unspliced HIV-1-specific RNA detection in peripheral blood mononuclear cells of individuals with varying CD4-positive lymphocyte counts.

Reverse transcriptase-polymerase chain amplification reactions (RT-PCR) were used to identify transcripts for HIV-1 structural and regulatory proteins in peripheral blood mononuclear cells of a cohort of 48 patients. At least one set of PCR primers was capable of detecting HIV-1 transcripts in 94% of patients. Unspliced gag-pol transcripts were detected with gag or pol primer sets in 60 and 63% of samples, respectively. A significant inverse correlation was noted between transcript identification with the gag primer set and the number of CD4-positive lymphocytes in the blood sample and the clinical stage of infection. Single-spliced env transcripts were identified in 44% of individuals. Multiple-spliced tat or nef transcripts were detected in 6.2 and 53% of individuals, respectively. These findings indicate that viral transcripts are expressed throughout the course of HIV-1 infection.

Base Sequence↗
PubMed2001

Circulating calcitonin and carcinoembryonic antigen m-RNA detected by RT-PCR as tumour markers in medullary thyroid carcinoma.

Detection of local relapse or metastasis in medullary thyroid carcinoma (MTC) continue to pose a major diagnostic challenge. Besides established diagnostic studies such as serum calcitonin (CT) and carcinoembryonic antigen (CEA), molecular detection of circulating tumour cells may be an additional diagnostic tool for the early detection of disease recurrence. We performed reverse transcription-polymerase chain reaction (RT-PCR) on blood samples from patients diagnosed with MTC disease using primers specific for CT and CEA, respectively. CT mRNA was not detectable in peripheral blood of all patients with MTC (n = 11) and all controls (n = 32). CEA mRNA was significantly more often detected patients with MTC (72.7%) than in controls (34.4%; p = 0.038; Fisher exact test). With an example of a patient with MTC and massive tumour mass in the neck we demonstrate the failure of detection of CT mRNA over a period of 6 months, whereas CEA mRNA could be detected in peripheral blood of this patient. As a consequence, CT mRNA detected by RT-PCR in the peripheral blood can not be recommended as a tumour marker in MTC. However, the use of carcinoembryonic mRNA may provide a significant improvement in diagnosis of recurrent disease in MTC.

Biomarkers, Tumor↗
PubMed2004

Assessment of CMV load in solid organ transplant recipients by pp65 antigenemia and real-time quantitative DNA PCR assay: correlation with pp67 RNA detection.

After bone marrow (BM) or solid-organ (SO) transplantation viremic Cytomegalovirus (CMV) infection is observed frequently. Quantitative assay of CMV in blood helps the management of this clinical condition. In the present report, 83 samples from 39 solid organ recipients, three CMV assays were compared simultaneously for the first time: the Nuclisens CMV pp67 assay (nucleic acid sequence-based amplification, NASBA), an "in-house" quantitative real-time PCR assay (TaqMan) for CMV DNA, and pp65 antigenemia. The relation between CMV DNA and pp65 antigenemia, the quantitative assays, was evaluated on a larger group including 251 blood samples from 118 solid organ recipients. Real-time PCR provided the best results; > or =130 CMV DNA copies/2 x 10(5) peripheral blood leukocytes (PBLs) predicted > or =1 pp65 antigen positive (Ag+) cell/2 x 10(5) PBLs. By taking pp65 antigenemia as the "gold standard," the sensitivity of CMV DNA quantitation and of the pp67 RNA assay were 0.95 and 0.20, respectively, while the corresponding specificity values were 0.50 and 0.93. When real-time PCR was considered as the "gold standard," the sensitivity and specificity of the pp65 antigenemia were 0.65 and 0.91, respectively. Among the three tests examined, the sensitivity of the pp67 RNA assay was the lowest. On the other hand, the pp67 RNA assay was highly specific and effective in pinpointing high viremia patients. The present report, by providing predictive values for all three diagnostic profiles, DNA load, antigenemia, and pp67RNA, is a contribution for validation of real-time PCR as a new standard for quantitative assessment of CMV viremia in clinical settings.

Antigens, Viral↗
PubMed1997

Melanoma-associated antigens as messenger RNA detection markers for melanoma.

Melanoma is heterogeneous for its biological properties and melanoma-associated antigens (MAAs). This diversity is partially observed in the expression of the MAAs involved with the melanin synthesis pathway. We therefore developed a sensitive multimarker reverse transcription-PCR plus Southern blot assay using five MAAs as molecular markers to detect primary and metastatic melanoma cells. Melanoma cell lines, melanocytes (cultured), primary and metastatic malignant melanoma tissues, and blood from patients with American Joint Committee on Cancer stage I-IV melanoma were assessed for tyrosinase, tyrosinase-related proteins 1 and 2, Pmel 17, and MART-1/Melan-A. All of the MAA mRNA markers were expressed in 100% of melanoma cell lines and cultured melanocytes, 74% of primary and metastatic tumors (excluding tumor-draining lymph nodes), 43% of tumor-involved lymph nodes, and 43% of patients' bloods. Hypomelanotic melanoma tissues expressed a lower frequency of individual mRNA markers. Overall, at least one mRNA marker was expressed in more than 86% of specimens assayed. Normal tissue specimens from patients and blood from normal volunteer donors were negative for MAA mRNA expression. The multimarker MAA reverse transcription-PCR plus Southern blot analysis was more reliable and sensitive than a single-molecular marker assay for the detection of melanoma cells. This molecular assay can also provide information on MAA mRNA expression of metastatic melanoma cells that may assist in monitoring the therapeutic efficacy of active specific immunotherapy toward specific MAA-bearing melanomas.

Antigens, Neoplasm↗
PubMed1993

Heterogeneity in MLL/AF-4 fusion messenger RNA detected by the polymerase chain reaction in t(4;11) acute leukemia.

We have designed a single polymerase chain reaction (PCR) primer pair that detects the MLL/AF-4 fusion mRNA encoded by the derivative 11 chromosome from t(4;11)(q21;q23) leukemia cells using the reverse transcriptase PCR technique. PCR amplification was possible in seven of seven cells studied. Sequencing of the amplified products showed three different breakpoints on 11q23 and three on 4q21, resulting in six unique fusion sequences. All fusion sequences maintained an open reading frame. The areas of the MLL and AF-4 genes that are conserved in all derivative 11 fusion RNAs and therefore likely to contribute to the function of the oncogenic fusion protein are centromeric regions of MLL through exon 6 (retaining the AT hook motif) and telomeric regions of AF-4 beginning at codon 491 (containing nuclear localization and GTP-binding motifs). A single primer pair was able to detect the derivative 11 fusion transcript in seven of seven cases of t(4;11) acute leukemia tested. Given the variability shown in specific fusion sequences, studies correlating differential exon usage with clinical parameters will require different fusion-specific oligonucleotides or PCR primer pairs.

Adolescent↗
PubMed1998

Performance of hepatitis C virus (HCV) antibody test systems in relation to HCV-RNA detection in the diagnosis of HCV infection.

BACKGROUND: Hepatitis C virus antibody (anti-HCV) test systems for screening and confirmation of blood donations have proved their value. The systems were later adopted for diagnosing patients suspected of hepatitis C. OBJECTIVES: 1) to study the clinical value of the recombinant immunoblot assay (RIBA) in routine diagnostics of patients suspected of HCV infection using HCV-PCR as the most definitive test and 2) to compare the performance of RIBA-2 with RIBA-3. MATERIALS: From May 1991 to August 1996 more than 4300 patients were tested for anti-HCV. All anti-HCV (EIA) positive patients were tested with RIBA-2 or RIBA-3 and HCV-PCR. RESULTS: We found no difference in the overall performance of RIBA-2 compared to RIBA-3. There was a tendency to fewer indeterminate results using RIBA-3 compared to RIBA-2 (5% vs. 9%), but this was not statistically significant. The NS5 band in RIBA-3 did not improve sensitivity or predictive value. Of RIBA-2 and RIBA-3 positive patients, 71% and 66% respectively were found to be HCV-RNA positive. Two samples that were negative using RIBA were HCV-RNA positive. CONCLUSION: RIBA testing in anti-HCV (EIA) positive patients added no clinically useful information to the screening results. We have therefore changed the diagnostic strategy so that all anti-HCV (EIA) positive patients are tested for HCV-RNA.

Hepacivirus↗
PubMed2000

High background levels compromise the use of cardiac troponin I RNA detection in peripheral blood as a diagnostic tool in cardiology.

The detection of cardiac troponins in peripheral blood as protein markers of myocardial infarction is a new diagnostic tool in the diagnosis of cardiac disease. In order to increase the sensitivity and specificity of this diagnostic approach, a reverse transcription polymerase chain reaction assay has been developed to detect the mRNA encoding cardiac troponin I from myocardial cells hypothetically released from damaged cardiac tissue. The detection is specific for cardiac troponin I mRNA, with no amplification of homologous sequences of other troponin I isoforms, i.e., troponin I from skeletal muscle cells. However, a strong amplification signal for cardiac troponin I mRNA was detected in samples of peripheral blood from healthy human volunteers. In patients with acute myocardial infarction or angina pectoris, the cardiac troponin I mRNA levels were not increased over background levels. In conclusion, a reverse transcription polymerase chain reaction approach based on the amplification of cardiac troponin I mRNA is not feasible in the diagnosis of cardiac diseases.

Angina Pectoris↗