Conversion-specific detection of DNA methylation using real-time polymerase chain reaction (ConLight-MSP) to avoid false positives

Methylated cytosines appear as sequence variations following bisulfite treatment and polymerase chain reaction (PCR) amplification. By using methylation-specific PCR (MSP), it is possible to detect methylated sequences in a background of unmethylated DNA with a high level of sensitivity. MSP is frequently used to identify methylated alleles in carcinogenesis, and may be combined with the TaqMan real-time PCR system, which uses fluorescence-based detection of amplification products during the amplification phase of the PCR and increases the sensitivity of detection (MethyLight). Sequences that have been incompletely converted during the bisulfite treatment are frequently coamplified during MSP, resulting in an overestimation of DNA methylation. The presence of amplified sequences originating from partially unconverted material may be determined by sequencing or by restriction digests or Southern blots of MSPs. Alternately, we have developed a method where the PCR and conversion assay are combined within a single TaqMan reaction by using an additional fluorescent probe directed against unconverted DNA (ConLight-MSP). We recommend that MSP detection always should include a step to detect unconverted DNA to avoid overestimation of the frequency or level of methylated DNA in the sample.     

成人急性髓性白血病SOCS-1基因及其甲基化的研究

目的：通过检测成人急性髓性白血病中SOCS．1基因表达水平及其甲基化水平,研究其在白血病发病中的作用。方法：运用甲基化特异性PCR（Methylation specificPCR,MSP）方法,对24例急性髓性白血病患者和4株白血病细胞株（Jurkat、Raji、U937、NALM17）,进行SOCS-1基因甲基化水平的研究;同时运用Real—timePCR法定量分析SOCS—1基因表达水平。以10例健康人为正常对照组。结果：24例成人急性髓性白血病患者中,15例有SOCS-1基因甲基化（62．5％）,而正常对照组无SOCS-1基因甲基化（0％）,二者有显著差异（P〈0．05）;SOCS-1基因甲基化组与无SOCS-1基因甲基化组相比较,其SOCS—1基因相对表达量明显减少（P口0．05）;与患者临床病理特征相结合比较,发现SOCS-1基因的甲基化与患者年龄、性别和病程阶段无相关。4株白血病细胞株中,Jurkat和U937表现有SOCS—1甲基化（50％）,Raji和NALM17无SOCS—1甲基化,前者SOCS-1基因表达量较后者也明显降低（P〈0．05）。结论：SOCS—1基因在成人急性髓性白血病中甲基化水平明显增高,且SOCS-1基因甲基化后表达水平受到抑制,提示SOCS-1基因及其甲基化在急性髓性白血病的发生发展中可能具有一定作用。     

Novel procedure for the detection of 5-methylcytosine.

Bisulfite converts non-methylated cytosine in DNA to uracil leaving 5-methylcytosine unaltered. In this communication, we present a new approach omitting the conventional PCR amplification step. Bisulfite-converted methylated DNA is directly sequenced. The effectiveness of the new protocol is demonstrated by using it for the detection of 5-methylation of cytosine residues introduced by three different DNA methyltransferases (M.HaeIII, M.HpaII and M.HhaI). A simple experimental system useful to determine the sequence specificity of DNA methyltransferases is also presented.     

Validation of a cotton-specific gene, Sad1, used as an endogenous reference gene in qualitative and real-time quantitative PCR detection of transgenic cottons

Genetically modified (GM) cotton lines have been approved for commercialization and widely cultivated in many countries, especially in China. As a step towards the development of reliable qualitative and quantitative PCR methods for detecting GM cottons, we report here the validation of the cotton (Gossypium hirsutum) endogenous reference control gene, Sad1, using conventional and real-time (RT)-PCR methods. Both methods were tested on 15 different G. hirsutum cultivars, and identical amplicons were obtained with all of them. No amplicons were observed when DNA samples from three species of genus Gossypium, Arabidopsis thaliana, maize, and soybean and others were used as amplified templates, demonstrating that these two systems are specific for the identification and quantification of G. hirsutum. The results of Southern blot analysis also showed that the Sad1 gene was two copies in these 15 different G. hirsutum cultivars. Furthermore, one multiplex RT-quantitative PCR employing this gene as an endogenous reference gene was designed to quantify the Cry1A(c) gene modified from Bacillus thuringiensis (Bt) in the insect-resistant cottons, such as Mon531 and GK19. The quantification detection limit of the Cry1A(c) and Sad1 genes was as low as 10 pg of genomic DNA. These results indicat that the Sad1 gene can be used as an endogenous reference gene for both qualitative and quantitative PCR detection of GM cottons.     

Bisulfite conversion-specific and methylation-specific PCR: a sensitive technique for accurate evaluation of CpG methylation

Methylation-specific PCR (MSP) is frequently used to distinguish methylated alleles in the genome. Sequences that have been incompletely converted during bisulfite treatment are frequently co-amplified during MSP. For accurate MSP, it is important to detect methylated sequences in a background of unconverted DNA with a high level of sensitivity. We report here sensitive techniques, bisulfite conversion-specific MSP (BS-MSP) to accurately evaluate CpG methylation. BS-MSP provides accurate results across a wide spectrum of bisulfite conversion levels. BS-MSP is also confirmed to be a useful technique for the routine analysis of clinical tumor specimens that were paraffin-embedded and microdissected. BS-MSP thus provides the powerful features of ease of use and compatibility with paraffin sections. We recommend that methylation analysis should include a step to eliminate unconverted DNA to avoid overestimation of the DNA methylation level in the samples.     

PCR detection of Listeria monocytogenes: a study of multiple factors affecting sensitivity

AIMS: To test, under comparable conditions, several parameters affecting sensitivity of PCR detection in order to establish a PCR procedure suitable for the routine detection of Listeria monocytogenes in food. METHODS AND RESULTS: Beef samples artificially inoculated were used to determine sensitivity of PCR detection under different parameters. As few as 1 CFU g(-1) were detected by DNA extraction using a DNeasy Tissue Kit (Qiagen GmhH, Hilden, Germany) of 1 ml aliquot and PCR amplification with primers directed to the hlyA gene. This PCR protocol was applied in 60 naturally contaminated foods, comparing two enrichment procedures with the traditional culture method. The highest number of positives was recorded by PCR following a 24-h pre-enrichment step at 30 degrees C and a 24-h enrichment step at 37 degrees C. Afterwards, it was applied in 217 naturally contaminated foods and 56 of them tested positive for L. monocytogenes in which only 17 tested positive using the culture method. CONCLUSIONS: The PCR procedure described has proved to be a rapid and sensitive method suitable for the routine analysis of different types of food. SIGNIFICANCE AND IMPACT OF THE STUDY: The method proposed for the detection of L. monocytogenes, has been validated in naturally contaminated food and is suitable to implement in the food industry.     

Methylation enrichment pyrosequencing: combining the specificity of MSP with validation by pyrosequencing

It has been suggested that detection of aberrant DNA methylation in clinical specimens such as sputum or saliva may be a valuable tumour biomarker. Any clinically applicable detection technique must combine high sensitivity with high specificity. In this study we describe methylation enrichment pyrosequencing (MEP), which benefits from the high sensitivity and specificity of methylation-specific PCR (MSP) but has a second, confirmatory, pyrosequencing step. The pyrosequencing reaction is rapid, relatively inexpensive and offers significant logistical advantages over previously described validation methods. As proof of principle, we illustrate MEP using assays of p16 and cyclin A1 promoters in a methylated DNA dilution matrix and also in a clinical setting using paired saliva and oral tumour specimens. Our results confirm that mis-priming of MSP, with subsequent false positive results, can occur frequently (perhaps 10%) in assays combining high numbers of PCR cycles and low concentrations of starting DNA. In our clinical example, MEP of saliva-derived DNA was more sensitive than standard non-methylation-specific pyrosequencing as illustrated using p16 and cyclin A1 promoter methylation assays.     

Sensitive Melting Analysis after Real Time- Methylation Specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection

DNA methylation changes that are recurrent in cancer have generated great interest as potential biomarkers for the early detection and monitoring of cancer. In such situations, essential information is missed if the methylation detection is purely qualitative. We describe a new probe-free quantitative methylation-specific PCR (MSP) assay that incorporates evaluation of the amplicon by high-resolution melting (HRM) analysis. Depending on amplicon design, different types of information can be obtained from the HRM analysis. Much of this information cannot be obtained by electrophoretic analysis. In particular, identification of false positives due to incomplete bisulphite conversion or false priming is possible. Heterogeneous methylation can also be distinguished from homogeneous methylation. As proof of principle, we have developed assays for the promoter regions of the CDH1, DAPK1, CDKN2A (p16^INK4a) and RARB genes. We show that highly accurate quantification is possible in the range from 100% to 0.1% methylated template when 25 ng of bisulphite-modified DNA is used as a template for PCR. We have named this new approach to quantitative methylation detection, Sensitive Melting Analysis after Real Time (SMART)-MSP.     

Highly sensitive determination of the methylated p16 gene in cancer patients by microchip electrophoresis

The p16 tumor suppressor gene is inactivated by promoter region hypermethylation in many types of tumor. Recent studies showed that aberrant methylation of the p16 gene is an early event in many tumors, especially in lung cancer, and may constitute a new biomarker for early detection and monitoring of prevention trials. We detected tumor-associated aberrant hypermethylation of the p16 gene in plasma and tissue DNA from 153 specimens using a modified semi-nested methylation-specific PCR (MSP) combining plastic microchip electrophoresis or slab gel electrophoresis, respectively. Specimens were from 79 lung cancer patients, 15 abdominal tumor patients, 30 positive controls and 30 negative controls. The results showed that the positive rate obtained by microchip electrophoresis was more than 26.6% higher and the same specificity was kept when compared with slab gel electrophoresis. The microchip electrophoresis can rapidly and accurately analyze the PCR products of methylated DNA and obviously improve the positive rate of diagnosis of cancer patients when compared with gel electrophoresis. This method with the high assay sensitivity might be used for detection of methylation of p16 gene and even to facilitate early diagnosis of cancer patients.     

成人急性髓性白血病SOCS-1 基因及其甲基化的研究

目的:通过检测成人急性髓性白血病中SOCS-1基因表达水平及其甲基化水平,研究其在白血病发病中的作用。方法:运用甲基化特异性PCR(Methylation specific PCR,MSP)方法,对24例急性髓性白血病患者和4株白血病细胞株(Jurkat、Raji、U 937、NALM 17),进行SOCS-1基因甲基化水平的研究;同时运用Real-time PCR法定量分析SOCS-1基因表达水平。以10例健康人为正常对照组。结果:24例成人急性髓性白血病患者中,15例有SOCS-1基因甲基化(62.5%),而正常对照组无SOCS-1基因甲基化(0%),二者有显著差异(P<0.05);SOCS-1基因甲基化组与无SOCS-1基因甲基化组相比较,其SOCS-1基因相对表达量明显减少(P﹤0.05);与患者临床病理特征相结合比较,发现SOCS-1基因的甲基化与患者年龄、性别和病程阶段无相关。4株白血病细胞株中,Jurkat和U 937表现有SOCS-1甲基化(50%),Raji和NALM 17无SOCS-1甲基化,前者SOCS-1基因表达量较后者也明显降低(P<0.05)。结论:SOCS-1基因在成人急性髓性白血病中甲基化水平明显增高,且SOCS-1基因甲基化后表达水平受到抑制,提示SOCS-1基因及其甲基化在急性髓性白血病的发生发展中可能具有一定作用。     

甲基化特异性PCR检测FMR1 和XIST基因甲基化实验方法的建立

建立一种快速、灵敏的检测脆性X智障基因（Fragile X mental retardation, FMR1）和X染色体失活基因（X chromosome inactivation,XIST）甲基化的方法,用亚硫酸氢钠和对苯二酚对基因组DNA进行脱氨基修饰。以修饰后的DNA为模板,用两套不同的引物对：1对甲基化特异性引物和1对非甲基化特异性引物扩增FMR1基因（CGG）n重复序列区、FMR1 和XIST 基因的启动子区。PCR产物进一步克隆、测序。以亚硫酸氢钠和对苯二酚脱氨基修饰后的DNA为模板,进行PCR扩增后的产物与预期基因目的基因片段大小相符合,无非特异性扩增产物。测序结果表明,FMR1、XIST基因中的非甲基化的C碱基转变为U碱基,而CpG岛被甲基化的C碱基不改变。成功地建立了检测FMR1、XIST甲基化的方法,为实验室诊断脆性X综合征提供了新的方法。     

Detection of methylated tissue factor pathway inhibitor 2 and human long DNA in fecal samples of patients with colorectal cancer in China

Background: To investigate the feasibility of detecting methylated tissue factor pathway inhibitor (TFPI2) and quantifying human long DNA with fluorescent quantitative Alu PCR in fecal DNA as a non-invasive screening tool for colorectal cancer (CRC). Materials and Methods: Methylation-specific PCR (MSP) was performed to analyze TFPI2 gene promoter methylation status in a blinded fashion in stool samples taken from 30 endoscopically diagnosed healthy controls, 20 patients with adenomas, and 60 patients with colorectal cancer. Real-time Alu PCR was used to quantify human long DNA. Results: The specificity of fecal TFPI2 MSP assay and long DNA assay was 100% and 83.3%, respectively. The sensitivity of fecal TFPI2 MSP assay and long DNA assay was 68.3% and 53.3%, respectively. The sensitivity of fecal DNA assay (either marker being positive) was 86.7%, which was high for CRC. Conclusions: Our results have demonstrated the feasibility of using TFPI2 methylation and quantify human long DNA with fluorescent quantitative Alu PCR in fecal samples as a new noninvasive test for CRC.     

Methylation of p16 and Ras association domain family protein 1a during colorectal malignant transformation

Accurate assessment of gene methylation in formalin-fixed, paraffin-embedded archived tissue (FF-PEAT) by microdissection remains challenging because the tissue volume is small and DNA is damaged. In addition, methods for methylation assessment, such as methylation-specific PCR (MSP), require sodium bisulfite modification (SBM) on purified DNA, which causes major loss of DNA. On-slide SBM, in which DNA is modified in situ before isolation of tumor cells, eliminates DNA purification steps and allows histology-oriented assessment of gene methylation. This study describes a protocol and use of on-slide SBM using 20 FF-PEAT of colorectal cancers with intratumoral adenoma components to detect accumulation of gene methylation during colorectal malignant transformation. Deparaffinized tissue sections were incubated in sodium bisulfite solution for 8 hours at 60 degrees C, stained with hematoxylin, and then microdissected. Proteinase K lysate was directly used as a template in subsequent PCR. Using on-slide SBM, 282-bp-long bisulfite direct sequencing was possible. Yield of modified DNA was 2.6-fold greater than standard SBM on average. The mean conversion rate was 97%, and false-positive or false-negative results were not observed in subsequent MSP. Intratumoral heterogeneity by accumulation of p16 and Ras association domain family protein 1a methylation during malignant transformation were shown by MSP comparing cancer with adenoma parts within a single section. On-slide SBM is applicable in most methylation studies using FF-PEAT. It allows detailed, intratumoral analysis of methylation heterogeneity within solid tumors. On-slide SBM will significantly improve our approach and understanding of epigenetic events in minimal disease and the carcinogenic process.     

Nonradioactive detection of telomerase activity using the telomeric repeat amplification protocol

The telomeric repeat amplification protocol (TRAP) is a two-step process for analyzing telomerase activity in cell or tissue extracts. Recent modifications of this sensitive assay include elimination of radioactivity by using a fluorescently labeled primer instead of a radiolabeled primer. In addition, the TRAP assay has been modified for real-time, quantitative PCR analysis. Here, we describe cost-effective procedures for detection of telomerase activity using a fluorescent-based assay as well as by using real-time PCR. These modified TRAP assays can be accomplished within 4 h (from lysis of samples to analysis of telomerase products).     

Development of a rapid,reliable and simple multiplex PCR assay for early detection of transgenic plant materials

Multiplex PCR is a variant of conventional PCR which includes two or more pairs of primers in a single reaction to amplify corresponding genes simultaneously. In this study, a reliable multiplex PCR analysis protocol was established for simple and fast detection of transgenes in plant materials. Two pairs of primers, corresponding to neomycin phosphotransferase gene and 1-aminocyclopropane-1-carboxylate synthase gene, were selected for target and resident gene respectively. The method bypasses routine DNA extraction, requires only very little amount of plant tissue and produces reliable results as shown by successful discrimination of transformed and nontransformed tobacco, tomato and kumquat materials. The method facilitates early identification of transgenic buds when they are still quite small.     

密码子优化小鼠socs-1基因及其在大肠杆菌中的表达

根据已报道的小鼠socs-1基因序列,依据大肠杆菌密码子偏爱性,设计并采用重叠PCR法合成了全长693bp的socs-1基因,将其克隆到表达载体pET-22b中构建表达载体pET-SOCS1。经IPTG诱导后,SDS-PAGE电泳显示此密码子优化后的基因可在大肠杆菌BL21(DE3)中高效表达。