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DNA damage by anticancer agents and its repair: mapping in cells at the subgene level with quantitative polymerase chain reaction.

The quantitative polymerase chain reaction (QPCR)-based assay was used to measure DNA damage and repair to a small (523 bp) fragment of the single-copy human N-ras gene in K562 cells. Compared with previous methods DNA preparation from treated cells and the subsequent detection of the radioactive product were considerably simplified. The results demonstrated that QPCR can be used to measure damage in a small gene segment, caused by cisplatin, nitrogen, and quinacrine mustards. Drug-DNA adducts produced by two novel minor groove binding, sequence-specific molecules (AT-486 and DSB-120) could be detected at physiologically relevant concentrations of drug. For both cisplatin and nitrogen mustard the concentrations required to cause damage in cells were higher than those needed to cause equivalent damage in isolated DNA. In contrast both AT-486 and quinacrine mustard caused more damage at equimolar concentrations in cells than in isolated DNA. DSB-120, which is closely related to AT-486, was found to be 15-fold less effective than the latter at causing damage in treated cells despite similar reactivity with isolated DNA. Repair of damage caused by quinacrine mustard to the same small gene fragment was found to proceed at a constant rate over 24 h. The QPCR assay presented here is a simple quantitative method to measure damage and repair in subgene functional units such as promoters, introns, and exons.

Antineoplastic Agents↗

Quantitative polymerase chain reaction using a DNA hybridization assay based on surface-activated microplates.

A method for DNA quantification on microplates based on the hybridization between single-stranded target and solid-phase bound capture DNA is presented. Binding of the capture DNA to the microplates was attained by surface activation using organosilanes. Detection of hybridized DNA was performed by an enzyme-linked assay taking advantage of the labeled target DNA. Basic test characteristics are described and application examples are given demonstrating its feasibility for a quantitative PCR (QPCR). The QPCR was carried out by coamplifying an immunoglobulin complementarity determining region 3 (CDR3)-coding plasmid DNA with a synthetic internal standard (IS). IS and plasmid CDR3 both shared primer binding sites and produced length-identical amplicons. The amplified DNA was quantified following differential hybridization with IS- and plasmid-specific capture probes. Based on the product ratios of plasmid to IS, the initial amounts of plasmid DNA were calculated. This way, QPCR was shown to be capable of detecting initial concentration differences of plasmid DNA of about 30%.

Base Sequence↗

Real-time PCR for quantifying Haemonchus contortus eggs and potential limiting factors.

The purpose of this study was to evaluate the practicality of using real-time PCR for quantifying feces-derived trichostrongyle eggs. Haemonchus contortus eggs were used to evaluate fecal contaminants, time after egg embryonation, and the presence of competing and non-competing DNAs as factors that might interfere with generating reproducible results during simplex and multiplex quantitative real-time PCR (QPCR). Real-time PCR results showed linear quantifiable amplification with DNA from five to 75 eggs. However, threshold cycle (C (T)) values obtained by amplification of DNA from egg numbers between 75 and 1,000 did not differ significantly. Inhibitors of QPCR were effectively removed during DNA extraction as exemplified by the absence of any improvement in C (T) values with bovine serum albumin or phytase treatments. Changes from egg embryonation could only be detected during the first 6 h. Noncompetitive DNA did not appear to impact amplification; however, in a multiplex reaction a competing trichostrongyle such as Cooperia oncophora can hinder amplification of H. contortus DNA, when present at tenfold greater amounts. This study demonstrates the usefulness of QPCR for amplification and quantification of trichostrongyle eggs, and identifies potential limitations, which may be addressed through multiplex assays or the addition of a standard: exogenous DNA target.

Animals↗

Determination of genetic sex in chinook salmon (Oncorhynchus tshawytscha) using the male-linked growth hormone pseudogene by real-time PCR.

This study used a real-time quantitative polymerase chain reaction (qPCR) method based on the growth hormone pseudogene (GHp) in chinook salmon (Oncorhynchus tshawytscha) to determine genetic sex. The GHp is present as a single copy in the genome of the male chinook salmon but is absent in the female, providing a means of using this real-time qPCR method to discriminate genetic sex. Comparisons between genomic DNA samples from 2 geographically distinct populations of chinook salmon (Columbia River, Washington, and Yukon River, Alaska) showed, within each population examined, that the males were clearly differentiated from the females. There were no interpopulation differences between males or females. The advantages of this real-time qPCR method are that it is rapid, is amenable to high sample throughput, and provides an accurate numerical value that allows comparisons between samples by statistical methods.

Alaska↗

Circadian expression of clock genes and clock-controlled genes in the rat retina.

The circadian expression patterns of genes encoding for proteins that make up the core of the circadian clock were measured in rat retina using real-time quantitative PCR (qPCR). Transcript levels of several genes previously used for normalization of qPCR assays were determined and the effect of ischemia-reperfusion on the expression of clock genes was studied. Statistically significant circadian changes in transcript levels were found for: Per2, Per3, Cry2, Bmal1, Rora, Rorb, and Rorc with changes ranging between 1.6- and 2.6-fold. No changes were found for Per1, Cry1, Clock, Rev-erb alpha, and Rev-erb beta. Significant differences in transcript levels were observed for several candidate reference genes: HPRT, GAPDH, rhodopsin, and Thy1 and, consequently, the use of these genes for normalization purposes in qPCR or Northern blots may lead to erroneous conclusions. Ischemia-reperfusion leads to a persistent decrease of Per1 and Cry2, which may be related to the selective degeneration of amacrine and ganglion cells. We conclude that while all clock genes are expressed in the retina, only a few show a clear circadian pattern.

Animals↗

Assessment of allele dosage at polymorphic microsatellite loci displaying allelic imbalance in tumors by means of quantitative competitive-polymerase chain reaction.

Analysis of allelic imbalance at polymorphic marker loci is usually employed to identify chromosomal regions affected by recurrent aberrations in tumor genomes. Such regions are likely to harbor genes involved in the onset and/or progression of cancer. Although often used to identify regions of loss of heterozygosity caused by deletions/rearrangements near tumor suppressor gene loci, allelic imbalance can also reflect regional amplification, indicating the presence of oncogenes. It is difficult to tell these two situations apart after ordinary polymerase chain reaction (PCR), but here we describe a method that distinguishes allelic loss from allelic gain. The level of allelic imbalance was determined by quantitative PCR (QPCR) in the presence of an internal control DNA that displayed a third allele at the locus studied. To validate the efficiency of allele quantitation, we analyzed an amplified region in a set of rat fibrosarcomas. In four tumor samples with amplification of the Met oncogene, we could show with QPCR that there was amplification of one of the alleles at a microsatellite marker located close to Met. QPCR may be useful for cancer studies because experiments may be predesigned for using either suitable microsatellite markers or the abundant and polymorphic poly-A tails of rodent identifier sequences.

Allelic Imbalance↗

METTL14-mediated m6A modification of CCNE1 accelerates progression of myelodysplastic syndromes via MAPK-ERK and PI3K-AKT signaling pathways.

BACKGROUND: N6-methyladenosine (m6A) is the most common RNA modification and plays a key role in the initiation, progression, and relapse of multiple cancers, including hematologic malignancies. However, the role of m6A and m6A regulatory genes in myelodysplastic syndromes (MDS) remains unclear. This study aims to elucidate the function and molecular mechanism of methyltransferase METTL14 in MDS. METHODS: RT-qPCR was used to assess the expression of multiple m6A regulators, focusing on METTL14 in MDS patients and cell lines. METTL14 overexpressing and knockdown cell lines were established, and CCK-8, EdU, and flow cytometry assays were performed to explore the biological functions of METTL14.Dot blot, MeRIP-Seq, MeRIP-qPCR, RT-qPCR, and Western blot were employed to investigate the underlying molecular mechanism. RESULTS: Dysregulation of multiple m6A regulators was observed in MDS, among which METTL14 was upregulated. Elevated METTL14 expression increases MDS risk and adverse prognosis, emerging as a biomarker for poor prognosis. METTL14 promoted proliferation and cell-cycle progression of MDS cells while inhibiting apoptosis; corresponding changes were observed in cell cycle and apoptosis markers. METTL14 regulated cellular m6A levels. Downstream targets of METTL14 were enriched in cell cycle-related pathways, with CCNE1 identified as a critical target. Knockdown of METTL14, actinomycin D, or S-adenosylhomocysteine treatment reduced CCNE1 mRNA and protein levels. Furthermore, METTL14 activated MAPK-ERK and PI3K-AKT signaling via CCNE1 in an m6A-dependent manner, thereby promoting proliferative MDS cells' capacity. CONCLUSIONS: This study delineates a METTL14/m6A/CCNE1 signaling axis in MDS progression and suggests that METTL14-mediated m6A modification may be a potential therapeutic target for MDS.

Humans↗

Quantitative multiplex real-time PCR for the sensitive detection of interferon beta gene induction and viral suppression of interferon beta expression.

Interferon-beta (IFN-beta) protein and activity can be detected by enzyme immunoassays and biological assays. However, precise quantification of low IFN-beta mRNA concentrations, which is advantageous for investigating IFN-beta gene expression in small tissue samples or during the early stage of a virus infection, remains a challenge. Therefore, we established a quantitative real-time PCR (qPCR) for IFN-beta and the housekeeping gene porphobilinogen deanimase (PBGD) in separated assays as well as in a multiplex procedure. Sensitivity for both the templates was less than 20 copies with an intra- and interassay variability of less than 5%. IFN-beta qPCR was utilized to optimize IFN-beta induction with dsRNA polyinosic-polycytidylic acid (poly I:C), delivered by a liposomal transfection agent for reproducible but low, non-cell-toxic IFN-beta concentrations. For studying coxsackievirus B3 (CVB3) interference with IFN-beta expression, CVB3 infected fibroblasts were induced with poly I:C. A significant reduction of IFN-beta mRNA but not PBGD mRNA was demonstrated 5 h after CVB3 infection, indicating a specific inhibition of IFN-beta expression by CVB3 on the mRNA level, in addition to previously reported effects on the translation/post-translation level. In conclusion, sensitive IFN-beta/PBGD multiplex qPCR proved to be a useful tool to study viral interaction with IFN-beta expression.

Gene Expression Regulation↗

Complement regulators in extraocular muscle and experimental autoimmune myasthenia gravis.

Complement activation at motor endplates is the primary effector mechanism in myasthenia gravis (MG). In this study, we evaluated whether differences in gene transcript levels and protein expression of cell-surface complement regulators could be a factor in the increased susceptibility of extraocular muscle (EOM) compared to other skeletal muscles to MG. Experimental autoimmune MG (EAMG) was induced in mice by administration of a monoclonal antibody (mAb) directed toward the acetylcholine receptor (AChR). Standard RT-PCR and real-time PCR (qPCR) were used to assess mRNA levels of decay-accelerating factor (DAF), CD59, and complement receptor 1-related gene/protein y (Crry). Gene transcript levels of the alpha- and gamma-subunits of the AChR were also evaluated by qPCR. Protein expression of the three intrinsic complement regulators at the neuromuscular junction was assessed by immunohistochemistry. Under constitutive conditions by RT-PCR, no significant differences were detected, but qPCR, EOM showed lower mRNA levels of all three complement regulators, but higher levels of alpha- and gamma-subunit gene transcripts. With EAMG, significant decreases in mRNA levels of all three complement regulators as well as AChR subunits occurred in EOM, but not in the diaphragm. Immunoreactivity for all three complement regulators was highly concentrated at diaphragm junctions, whereas it was less intense or absent at EOM junctions. With EAMG, immunoreactivity for Crry and DAF increased at diaphragm junctions and for DAF at EOM junctions. Diminished intrinsic complement regulatory activity may contribute to the susceptibility of EOM to MG. Our findings suggest that complement inhibitor-based therapies could be useful in treating ocular manifestations of MG.

Animals↗

Laser microdissection of immunolabeled astrocytes allows quantification of astrocytic gene expression.

Astrocytes represent the major glial cell population within the central nervous system. In order to elucidate the function of astrocytes under physiological conditions and during the course of neurological disease, astrocytic gene expression profiling is necessary. However, since astrocytes form an intimately connected network with neurons and other cell types in the brain, gene expression analysis of astrocytes with a sufficient degree of cellular specificity is difficult. Here we are presenting a rapid and, thus, RNA preserving immunostaining protocol for the detection of astrocytes in rodent brain. This protocol can readily be combined with laser microdissection (Leica AS LMD platform) and quantitative RT-PCR (qPCR). Employing this method, we studied changes in glial fibrillary acidic protein (GFAP) expression in astrocytes of mouse entorhinal cortex following entorhinal cortex lesion. Using laser microdissection, astrocytes (n = 60) were collected in the tissue surrounding the lesion, the entorhinal cortex contralateral to the lesion, and in unlesioned control animals. Changes in GFAP mRNA were quantified using qPCR. GFAP mRNA levels were 82-fold higher in astrocytes of lesioned animals at the site of the lesion compared to GFAP mRNA levels in entorhinal cortex astrocytes of control mice. GFAP mRNA levels were only slightly elevated at the contralateral side (lesioned animals). This optimized protocol for immunolabeling and laser microdissection of astrocytes followed by qPCR allows quantification of astrocytic gene expression levels with a high degree of cellular specificity. It may similarly be employed in different settings where other cell types need to be identified and microdissected for gene expression profiling.

Animals↗

Development of comprehensive functional genomic screens to identify novel mediators of osteoarthritis.

OBJECTIVE: The aim of this study was to develop high-throughput assays for the analysis of major chondrocyte functions that are important in osteoarthritis (OA) pathogenesis and methods for high-level gene expression and analysis in primary human chondrocytes. METHODS: In the first approach, complementary DNA (cDNA) libraries were constructed from OA cartilage RNA and full-length clones were selected. These cDNAs were transferred into a retroviral vector using Gateway Technology. Full-length clones were over-expressed in human articular chondrocytes (HAC) by retroviral-mediated gene transfer. The induction of OA-associated markers, including aggrecanase-1 (Agg-1), matrix metalloproteinase-13 (MMP-13), inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), collagen IIA and collagen X was measured by quantitative real-time polymerase chain reaction (QPCR). Induction of a marker gene was verified by independent isolation of 2-3 clones per gene, re-transfection followed by QPCR as well as nucleotide sequencing. In the second approach, whole cDNA libraries were transduced into chondrocytes and screened for chondrocyte cluster formation in three-dimensional agarose cultures. RESULTS: Using green fluorescent protein (eGFP) as a marker gene, it was shown that the retroviral method has a transduction efficiency of >90%. A total of 40 verified hits were identified in the QPCR screen. The first set of 19 hits coordinately induced iNOS, COX-2, Agg-1 and MMP-13. The most potent of these genes were the tyrosine kinases Axl and Tyro-3, receptor interacting kinase-2 (RIPK2), tumor necrosis factor receptor 1A (TNFR1A), fibroblast growth factor (FGF) and its receptor FGFR, MUS81 endonuclease and Sentrin/SUMO-specific protease 3. The second set of seven hits induced both Agg-1 and MMP-13 but none of the other markers. Five of these seven genes regulate the phosphoinositide-3-kinase pathway. The most potently induced OA marker was iNOS. This marker was induced 20-500 fold by seven genes. Collagen IIA was also induced by seven genes, the most potent being transforming growth factor beta (TGFbeta)-stimulated protein TSC22, vascular endothelial growth factor (VEGF) and splicing factor 3a. This screening assay did not identify inducers of collagen X. The second chondrocyte cluster formation screen identified 14 verified hits. Most of the genes inducing cluster formation were kinases. Additional genes had not been previously known to regulate chondrocyte cluster formation or any other chondrocyte function. CONCLUSIONS: The methods developed in this study can be applied to screen for genes capable of inducing an OA-like phenotype in chondrocytes on a genome-wide scale and identify novel mediators of OA pathogenesis. Thus, coordinated functional genomic approaches can be used to delineate key genes and pathways activated in complex human diseases such as OA.

Cartilage, Articular↗

Real-time quantitative PCR-based serum neutralization test for detection and titration of neutralizing antibodies to chicken anemia virus.

Detection and titration of chicken anemia virus (CAV)-neutralizing antibodies has relied on tedious, time-consuming passaging of infected cells, or subjective recognition of cytopathic effect in individual cells, because CAV replicates in culture only in lymphoblastoid cell lines, and thus generates no plaques. This paper describes a rapid method, in which CAV genomes in infected cells are quantitated by qPCR 3-4 days postinfection (p.i.), without passaging cells. Three sera, weakly positive with a commercial CAV ELISA kit, from broiler chickens immunized with a commercial CAV vaccine, were used to develop the assay. Virus neutralization titers of these sera were determined using two different CAV-susceptible cell lines (MDCC-MSB1 and MDCC-CU147) by the conventional method of passaging cells infected with 10,000 TCID(50) CAV per well, and by qPCR-based methods using cells infected with 100 or 10,000 TCID(50) per well in 24-well or 96-well plates. The method was also adapted to conventional PCR. The positive sera exhibited virus neutralization activity at dilutions ranging from 1:10 to 1:320 by the various assays. Although virus neutralization titers differed somewhat depending on the assay conditions used, the relative order of the titers of the three positive sera was the same for all assays. The qPCR-based assays are as sensitive and more rapid for detection of neutralizing antibody than the conventional assay based on passaging infected cells, and more sensitive for detection of low-level CAV antibodies than a commercial blocking ELISA.

Animals↗

Estimation of the number of infectious measles viruses in live virus vaccines using quantitative real-time PCR.

The potency of live attenuated virus vaccines is determined by counting or titrating viable viruses in cell cultures. These classical potency tests have the drawback that they are time consuming and laborious and show a high laboratory-to-laboratory variation. In the present study we describe the development and validation of a fast method to measure the potency of measles in trivalent measles, mumps and rubella (MMR) vaccines using quantitative real-time PCR (qPCR). Vero cells were infected with serial dilutions of a trivalent vaccine or a trivalent reference with known potency. Virus was allowed to replicate and subsequently replicated virus was quantitated by qPCR using the LightCycler technology. The virus titer in vaccine samples was estimated against reference preparations using parallel line analysis. In comparison to the plaque assay, the qPCR infectivity assay was faster and less laborious, while accuracy and intermediate precision were similar.

Animals↗

Detection and quantitation of Solenopsis invicta virus in fire ants by real-time PCR.

A quantitative real-time PCR (QPCR) method was developed to detect and quantify the amount of Solenopsis invicta virus (SINV) infecting individual ants of S. invicta. The two-step method utilized a gene-specific oligonucleotide primer targeting the SINV RNA-dependent RNA polymerase (RdRp) for cDNA synthesis. Dithiothreitol used in the cDNA synthesis step was found to significantly decrease the detection sensitivity for SINV RdRp and was therefore omitted. SINV RdRp cDNA was then quantified by QPCR using SYBR Green dye and a standard curve generated from SINV RdRp plasmid clones. A standard curve was successfully constructed from clones of the SINV RdRp region. A strong linear relationship [r2=0.998; y=(-3.63+/-0.37)x+(39.19+/-1.33)] between C(T) and starting SINV RdRp copy number was observed within a dynamic range of 5-5 x 10(6) copies. SINV RdRp copy number was determined with the optimized QPCR method in individual S. invicta ants taken from an infected field colony. Worker ants exhibited the highest RdRp copy number (2.1 x 10(9) copies/worker ant) and pupae exhibited the lowest (4.2 x 10(2) copies/pupa). Mean RdRp copy number was lowest in early larvae and pupae. Overall, SINV RdRp copy number increased through larval development, sharply declined during pupation, then sharply increased in adults.

Animals↗

Development of quantitative real-time PCR assays to detect Rickettsia typhi and Rickettsia felis, the causative agents of murine typhus and flea-borne spotted fever.

Rickettsia typhi and Rickettsia felis are the etiologic agents of murine typhus and flea-borne spotted fever, respectively. We have constructed two quantitative real-time polymerase chain reaction (qPCR) assays to detect these pathogenic rickettsiae. The qPCR assays were developed utilizing unique sequences of the R. typhi and R. felis outer membrane protein B genes (ompB) to design the specific primers and molecular beacon probes. The assays were found to be species-specific and did not yield false-positive reactions with nucleic acid from other rickettsiae, orientiae, neorickettsiae or unrelated bacteria. In addition, the assays were sensitive enough to detect three target sequence copies per reaction and were capable of detecting R. typhi and R. felis nucleic acid in the cat flea, Ctenocephalides felis. These results demonstrate that two sensitive and specific qPCR assays have been successfully developed to detect and enumerate R. typhi and R. felis.

Animals↗

Enumeration of specific bacterial populations in complex intestinal communities using quantitative PCR based on the chaperonin-60 target.

We used qPCR and the target gene chaperonin-60 (cpn60) to enumerate Clostridium perfringens genomes in DNA extracts from contents of the chicken gastrointestinal tract with the aim of optimizing this methodology to enumerate any bacterium of interest. To determine the most accurate protocols for determining target species abundance, we compared various DNA extraction methods in combination with four methods for producing standard curves. Factors affecting accuracy included the co-purification of PCR inhibitors and/or fluorescence quenchers and the yield of target DNA in the extract. Anion exchange chromatography of the spiked test samples enabled accurate enumeration of C. perfringens using a standard curve comprised of a plasmid containing a fragment of C. perfringens cpn60. We used qPCR to enumerate C. perfringens and other intestinal bacteria in ileum and cecum samples from chickens that had been challenged with C. perfringens and compared the results with viable counts on corresponding selective agars. We conclude that qPCR-based molecular enumeration of target species in the gastrointestinal tract is feasible, but care must be taken in order to mitigate the effects of confounding factors that can affect the apparent cell count.

Animals↗

Selective enrichment and detection of mycobacterial DNA in paucibacillary specimens.

A major challenge for tuberculosis control is mycobacterial detection in paucibacillary disease, particularly in pediatric, extrapulmonary and smear-negative pulmonary infections. We developed a simple and efficient DNA extraction and real-time quantitative PCR (qPCR) protocol for mycobacterial detection and quantification in paucibacillary specimens. The method was refined using an in vitro model mimicking blood specimens which are characterized by the presence of numerous qPCR inhibitors. Mycobacterial DNA detection in blood is of interest given the high sensitivity we previously reported using conventional PCR in blood of patients with tuberculosis lymphadenitis. Mechanical lysis of mycobacteria in the presence of an organic solvent provided the highest sensitivity. Mycobacterial DNA amplification was compromised when the human:bacterial genome ratio was at least 190:1. Separation of the specimen into bacterial- and host-rich fractions prior to DNA extraction improved mycobacterial DNA detection by 30%. Preliminary testing of our protocol in smear-negative, culture-positive specimens (gastric and lymph node aspirates, pleural and cerebrospinal fluid, and blood) confirmed the applicability of our technique to a range of paucibacillary specimens for the detection, quantification and speciation (M. tuberculosis versus M. avium) of mycobacteria, several weeks before culture results were available. Our protocol provides a novel, efficient and simple strategy to improve the performance of qPCR in paucibacillary specimens, including those with excess human DNA background. This tool is useful to study the pathophysiology of early pulmonary or occult tuberculosis, and for more rapid and accurate diagnosis in difficult to diagnose infections.

Benzothiazoles↗

Use of a real time PCR assay for detection of the ctxA gene of Vibrio cholerae in an environmental survey of Mobile Bay.

Toxigenic Vibrio cholerae, the etiological agent of cholera, is a natural inhabitant of the marine environment and causes severe diarrheal disease affecting thousands of people each year in developing countries. It is the subject of extensive testing of shrimp produced and exported from these countries. We report the development of a real time PCR (qPCR) assay to detect the gene encoding cholera toxin, ctxA, found in toxigenic V. cholerae strains. This assay was tested against DNA isolated from soil samples collected from diverse locations in the US, a panel of eukaryotic DNA from various sources, and prokaryotic DNA from closely related and unrelated bacterial sources. Only Vibrio strains known to contain ctxA generated a fluorescent signal with the 5' nuclease probe targeting the ctxA gene, thus confirming the specificity of the assay. In addition, the assay was quantitative in pure culture across a six-log dynamic range down to <10 CFU per reaction. To test the robustness of this assay, oysters, aquatic sediments, and seawaters from Mobile Bay, AL, were analyzed by qPCR and traditional culture methods. The assay was applied to overnight alkaline peptone water enrichments of these matrices after boiling the enrichments for 10 min. Toxigenic V. cholerae strains were not detected by either qPCR or conventional methods in the 16 environmental samples examined. A novel exogenous internal amplification control developed by us to prevent false negatives identified the samples that were inhibitory to the PCR. This assay, with the incorporated internal control, provides a highly specific, sensitive, and rapid detection method for the detection of toxigenic strains of V. cholerae.

Alabama↗