Quantitative analysis of cytokeratin 20 gene expression using RT-PCR and capillary electrophoresis with fluorescent DNA detection

Comparison of methods for quantification of subtle splice variants

Alternative splicing is capable of generating multiple mRNA variants from a single gene and is hence a key mediator of molecular diversity generated at the transcript level. Consequently, delivering quantitative information on the fractions of splice variants is essential for the understanding of their biological roles. Here we compare techniques for subtle splice variant quantification that are able to resolve length differences as small as one nucleotide: PAGE with ethidium-bromide densitometry, pyrosequencing, and CE-LIF. We give comprehensive descriptions of assay designs and calibration procedures and present an evaluation of these methods in terms of accuracy, reproducibility and applicability. We also examined template concentrations and reverse transcription-coupled PCR conditions as potential cause of biased results as they were observed for extreme low template concentrations and/or PCR amplicons with size differences of 195 nt. As proof of concept, we determine the splice ratios of variants differing by 3 and 12 nt in five human tissues. We demonstrate that CE-LIF is the most precise and also the most labor- and time-efficient method.

Curcumin induces apoptosis and inhibits growth of human Burkitt's lymphoma in xenograft mouse model

Curcumin, a natural compound extracted from rhizomes of curcuma Curcuma species, has been shown to possess potent anti-inflammatory, anti-tumor and anti-oxidative properties. However, the mechanism of action of the compound remains poorly understood. In this report, we have analyzed the effects of curcumin on the cell proliferation of Burkitt's lymphoma Raji cells. The results demonstrated that curcumin could effectively inhibit the growth of Raji cells in a dose- and time-dependent manner. Further studies indicated that curcumin treatment resulted in apoptosis of cells. Biochemical analysis showed that the expression of Bax, Bid and cytochrome C were up-regulated, while the expression of oncogene c-Myc was down regulated after curcumin treatment. Furthermore, poly (ADP-ribose) polymerase (PARP) cleavage was induced by the compound. Interestingly, the antiapoptotic Bcl-2 expression was not significantly changed in Raji cells after curcumin treatment. These results suggested that the mechanism of action of curcumin was to induce mitochondrial damage and therefore led to Raji cell apoptosis. We further investigated the in vivo effects of curcumin on the growth of xenograft tumors in nude mice. The results showed that curcumin could effectively inhibit tumor growth in the xenograft mouse model. The overall results showed that curcumin could suppress the growth of Burkitt's lymphoma cells in both in vitro and in vitro systems.

Quantitative RT-PCR detection of colorectal tumor cells in peripheral blood--a systematic review

BACKGROUND

Twenty percent to 40% of patients with node-negative colorectal cancer die of metastatic disease. Detection of cancer cell dissemination has been proposed as a tool to select patients at highest risk for recurrence. In this review, we summarize the evidence for detection with quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) assays of circulating tumor cells (CTCs) in peripheral blood of colorectal cancer patients.

MATERIALS AND METHODS

Pubmed and Embase were systematically searched for all English publications relevant to circulating cancer cells, peripheral blood, quantitative RT-PCR (q-RT-PCR), and colorectal cancer. Cross-references and the "related articles" function were used to broaden the search. Manuscripts reporting on the results of nonquantitative RT-PCR assays were excluded. The study methodology, CTCs detection rates in peripheral blood, and prognostic value were reviewed.

RESULTS

Twelve manuscripts on qRT-PCR were retrieved. Stage dependence was found for detection of CTCs in four of 10 studies. From univariate analysis performed for disease-free survival and overall survival in 4 of 12 studies, there was evidence (P < 0.05) for an effect of the detection of CTCs with qRT-PCR. None of the included trials identified detection of CTCs in peripheral blood as an independent predictor of survival.

CONCLUSION

Quantification of CTCs in peripheral blood holds promise in predicting stage and outcome in colorectal cancer patients. At present, evidence from the literature is too scarce to integrate quantitative RT-PCR assays to detect CTCs into the management of colorectal cancer.

EC. Direct quantification of gene expression using capillary electrophoresis with laser-induced fluorescence

Quantification of gene expression provides valuable information regarding the response of cells or tissue to stimuli and often is accomplished by monitoring the level of messenger RNA (mRNA) being transcribed for a particular protein. Although numerous methods are commonly used to monitor gene expression, including Northern blotting, real-time polymerase chain reaction, and RNase protection assay, each method has its own drawbacks and limitations. Capillary electrophoresis with laser-induced fluorescence (CE-LIF) can reduce protocol time, eliminate the need for radioactivity, and provide superior sensitivity and dynamic range for quantification of RNA. In addition, CE-LIF can be used to directly determine the amount of an RNA species present, something that is difficult and not normally accomplished using current methods. Gene expression is detected using a fluorescently labeled riboprobe specific for a given RNA species. This direct approach was validated by analyzing levels of 28S RNA and also used to determine the amount of discoidin domain receptor 2 mRNA in cardiac tissue.

Quantitation of mRNA levels of steroid 5alpha-reductase isozymes in the rat brain by "one-step" RT-PCR and capillary electrophoresis

The enzyme 5alpha-reductase (5alpha-R) is present in many mammalian tissues, including the brain. The physiological importance of 5alpha-R in the brain derives from its capability to convert testosterone (T) to a more potent androgen, dihydrotestosterone (DHT), and to convert progesterone to its 5alpha-reduced derivative, precursors of allopregnanolone, potent allosteric modulator of the gamma-aminobutyric acid receptor (GABA(A)-R). 5alpha-R occurs as two isoforms, 5alpha-R type 1 (5alpha-R1) and 5alpha-R type 2 (5alpha-R2). We present an accurate, rapid, and modestly labor-intensive method to precisely quantitate 5alpha-R mRNA species in the cerebral cortex of the rat. This approach combines the high specificity of "one-step" reverse transcription-polymerase chain reaction (RT-PCR) with the sensitivity of laser-induced fluorescence capillary electrophoresis (LIF-CE). Both cDNA synthesis and PCR amplification are performed with the same enzyme and site-specific primers, improving the efficiency of cDNA synthesis. The specific target mRNA and a mimic DNA fragment, used as a competitive internal standard, were co-amplified in a single reaction in which the same primers are used. The method presented in this paper enables a more efficient quantitative determination of 5alpha-R mRNA isozymes, and may lead to a better understanding of the role of 5alpha-R isozymes in the physiology of the central nervous system.

Quantitation of mRNA levels of steroid 5α-reductase isozymes in the rat brain by “one-step” RT-PCR and capillary electrophoresis

The enzyme 5alpha-reductase (5alpha-R) is present in many mammalian tissues, including the brain. The physiological importance of 5alpha-R in the brain derives from its capability to convert testosterone (T) to a more potent androgen, dihydrotestosterone (DHT), and to convert progesterone to its 5alpha-reduced derivative, precursors of allopregnanolone, potent allosteric modulator of the gamma-aminobutyric acid receptor (GABA(A)-R). 5alpha-R occurs as two isoforms, 5alpha-R type 1 (5alpha-R1) and 5alpha-R type 2 (5alpha-R2). We present an accurate, rapid, and modestly labor-intensive method to precisely quantitate 5alpha-R mRNA species in the cerebral cortex of the rat. This approach combines the high specificity of "one-step" reverse transcription-polymerase chain reaction (RT-PCR) with the sensitivity of laser-induced fluorescence capillary electrophoresis (LIF-CE). Both cDNA synthesis and PCR amplification are performed with the same enzyme and site-specific primers, improving the efficiency of cDNA synthesis. The specific target mRNA and a mimic DNA fragment, used as a competitive internal standard, were co-amplified in a single reaction in which the same primers are used. The method presented in this paper enables a more efficient quantitative determination of 5alpha-R mRNA isozymes, and may lead to a better understanding of the role of 5alpha-R isozymes in the physiology of the central nervous system.

Quantitation of Transgenic Bt Event-176 Maize Using Double Quantitative Competitive Polymerase Chain Reaction and Capillary Gel Electrophorsesis Laser-Induced Fluorescence

In this work, a new procedure useful to quantitatively analyze genetically modified organisms (GMOs) in foods is described and applied to analyze transgenic Bt Event-176 maize. The method developed consists of coamplifications of specific DNA maize sequences with internal standards using quantitative competitive PCR (QC-PCR). The QC-PCR products are quantitatively analyzed using a capillary gel electrophoresis (CGE) with laser-induced fluorescence detection (LIF) method developed at our laboratory that utilizes a physically adsorbed coating. The CGE-LIF procedure allows the use of internal standards differing by only 10 bp from the original target fragments, to our knowledge, the smallest size difference that can be found in the bibliography for QC-PCR of GMOs. A spectrofluorometric procedure using ROX reference dye is proposed to solve calibration problems of input DNA concentration. It is demonstrated that the use of ROX drastically enhances the accuracy of the quantitative analysis by QC-PCR. Reproducibility of analysis times and corrected peak areas (measured as target/competitor PCR products ratio) for the CGE-LIF separations are determined to be better than 0.91 and 1.93% (RSD, n = 15) respectively, for three different days. It is shown that CGE-LIF provides better resolution and a signal/noise ratio improvement of approximately 700-fold compared to slab gel electrophoresis. The good possibilities in terms of quantitative analysis of GMOs provided by this new method are confirmed by determining the Bt Event-176 maize content in certified reference maize powder and food samples of known composition. This procedure opens the possibility for accurate quantitation of multiple GMOs in a single run.

Quantitative real-time RT-PCR for detection of disseminated tumor cells in peripheral blood of patients with colorectal cancer using different mRNA markers

The detection of disseminated tumor cells in peripheral blood from colorectal cancer patients by RT-PCR could be an attractive method for selecting patients for adjuvant therapy. We here report on real-time RT-PCR assays (LightCycler) to quantitate potential mRNA markers. We investigated specimens from colon carcinoma and normal colon mucosa tissues, cell lines, blood samples from 129 patients with colorectal cancer (all stages) and 58 reference blood samples (healthy donors, persons suffering from inflammatory bowel or infectious diseases). The expression profile in tissues showed high values for CEA and CK20, whereas in cell lines ProtM was predominant. All markers were detected in reference and patient blood samples (ProtM, 22, 17%; CEA, 84, 86%; CK20, 85, 88%). After quantitative analysis, the definition of cutoff values for each marker and the combination of markers, 13% of patients were judged to have elevated marker concentrations in their blood, from which only 6 had values significantly differing from cutoff value. There were no differences between stages of disease. In the case of 19 patients, investigated prior to and 1 week after surgery, 2 samples revealed a significant postoperative increase in CEA or CK20 mRNA concentration. In spite of high expression levels in tissues and cell lines, we were not able to differentiate satisfyingly mRNA markers originating from tumor cells and those from illegitimate transcription in hematopoetic cells in blood. We conclude that either copy numbers of analyzed markers in circulating tumor cells are not sufficient for detection or, more probably, peripheral blood is not a suitable compartment for detection of tumor cells in colorectal cancer.

Effect of blood sample handling and reverse transcriptase-polymerase chain reaction assay sensitivity on detection of CK20 expression in healthy donor blood

Data concerning the specificity of cytokeratin 20 (CK20) as a reverse transcriptase-polymerase chain reaction analysis (RT-PCR) marker to detect disseminated tumor cells in blood are conflicting. Underlying causes for these discrepancies need to be determined to clarify the significance of CK20 detection. Because differences in RT-PCR assays and blood sample handling may be important, their influence on CK20 detection was studied. Using a series of healthy donor blood samples spiked with colon tumor cells, the authors compared the sensitivities of two conventional PCRs with different primer sets and a quantitative LightCycler PCR (Roche Diagnostics GmbH, Penzberg, Germany). Additionally, the influence of sample collection and preparation on assay specificity was studied by examining CK20 expression in the mononuclear cell fraction (MNC) of the first and the second aliquot of blood drawn from healthy donors and in the granulocyte cell fraction. At the concentration of one spiked tumor cell/mL blood, the CK20 detection frequency varied from 17% and 67% for the conventional to 78% for the LightCycler PCR. In the unspiked samples, CK20 was detected in 0% and 8% of the conventional and in 11% of the LightCycler PCR tests. Quantitative analysis revealed that CK20 was expressed at a high level in the granulocyte samples. The results demonstrate that differences in assay sensitivity and sample handling influence CK20 detection in blood.

Identification of nine alternatively spliced alpha2,3-sialyltransferase, ST3Gal IV, transcripts and analysis of their expression by RT-PCR and laser-induced fluorescent capillary electrophoresis (LIF-CE) in twenty-one human tissues

In order to characterise the candidate alpha2,3-sialyltransferases necessary for biosynthesis of the selectin ligand SLe(x) and related antigens we have cloned and sequenced, from peripheral blood leukocytes of single individuals, various transcripts from the human ST3Gal III, IV and VI genes. Our clones have revealed a considerable heterogeneity in transcript isoforms. Among our ST3Gal IV clones we isolated nine alternatively spliced transcripts covering the coding region of the human ST3Gal IV gene (A1, A1 - 12, A1 + 18, A2, A2 - 12, A2 + 18, B, B - 12 and B + 18). Five of these isotranscripts A1 - 12, A1 + 18, A2 - 12, A2 + 18 and B + 18 have not been described before. In order to investigate if the alternatively spliced isotranscripts were specific for human PBL, we analysed the expression by RT-PCR and laser-induced fluorescent capillary electrophoresis (LIF-CE) in twenty other human tissues. We found a tissue specific expression of ST3Gal IV A1, A1 - 12, A1 + 18, A2, A2 - 12, A2 + 18 and B + 18 as well as a general expression of ST3Gal IV B and B - 12 isotranscripts in all tissues examined.