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1.  High recovery of cell-free methylated DNA based on a rapid bisulfite-treatment protocol 
BMC Molecular Biology  2012;13:12.
Background
Detection of cell-free methylated DNA in plasma is a promising tool for tumour diagnosis and monitoring. Due to the very low amounts of cell-free DNA in plasma, analytical sensitivity is of utmost importance. The vast majority of currently available methods for analysing DNA methylation are based on bisulfite-mediated deamination of cytosine. Cytosine is rapidly converted to uracil during bisulfite treatment, whereas 5-methylcytosine is only slowly converted. Hence, bisulfite treatment converts an epigenetic modification into a difference in sequence, amenable to analysis either by sequencing or PCR based methods. However, the recovery of bisulfite-converted DNA is very poor.
Results
Here we introduce an alternative method for the crucial steps of bisulfite treatment with high recovery. The method is based on an accelerated deamination step and alkaline desulfonation in combination with magnetic silica purification of DNA, allowing preparation of deaminated DNA from patient samples in less than 2 hours.
Conclusions
The method presented here allows low levels of DNA to be easily and reliably analysed, a prerequisite for the clinical usefulness of cell-free methylated DNA detection in plasma.
doi:10.1186/1471-2199-13-12
PMCID: PMC3324385  PMID: 22448717
2.  Plasma vitamins B2, B6, B12, and related genetic variants as predictors of colorectal cancer risk 
Background
B-vitamins are essential for one-carbon metabolism and have been linked to colorectal cancer (CRC). Although associations with folate have frequently been studied, studies on other plasma vitamins B2, B6, and B12 and CRC are scarce or inconclusive.
Methods
Nested case-control study within the European Prospective Investigation into Cancer and Nutrition, including 1365 incident CRC cases and 2319 controls matched for study center, age, and sex. We measured the sum of B2 species riboflavin and flavin mononucleotide, and the sum of B6 species pyridoxal 5′-phosphate, pyridoxal, and 4-pyridoxic acid as indicators for vitamin B2 and B6 status, as well as vitamin B12 in plasma samples collected at baseline. In addition, we determined eight polymorphisms related to one-carbon metabolism. Relative risks (RRs) for CRC were estimated using conditional logistic regression, adjusted for smoking, education, physical activity, BMI, alcohol consumption, and intakes of fiber, red- and processed meat.
Results
RRs comparing highest to lowest quintile (95% confidence interval, Ptrend) were: 0.71 (0.56–0.91, 0.02) for vitamin B2, 0.68 (0.53–0.87, <0.001) for vitamin B6, and 1.02 (0.80–1.29, 0.19) for vitamin B12. The associations for vitamin B6 were stronger in males who consumed ≥ 30g alcohol/day. The polymorphisms were not associated with CRC.
Conclusions
Higher plasma concentrations of vitamins B2 and B6 are associated with a lower CRC risk.
Impact
This European population-based study is the first to indicate that vitamin B2 is inversely associated with CRC, and is in agreement to previously suggested inverse associations of vitamin B6 with CRC.
doi:10.1158/1055-9965.EPI-10-0407
PMCID: PMC3025315  PMID: 20813848
Plasma vitamins B2, B6, and B12; genetic variants; colorectal cancer; prospective study
3.  Complement activation capacity in plasma before and during high-dose prednisolone treatment and tapering in exacerbations of Crohn's disease and ulcerative colitis 
BMC Gastroenterology  2005;5:31.
Background
Ulcerative colitis (UC) and Crohn's disease (CD) are characterized by intestinal inflammation mainly caused by a disturbance in the balance between cytokines and increased complement (C) activation. Our aim was to evaluate possible associations between C activation capacity and prednisolone treatment.
Methods
Plasma from patients with exacerbations of UC (n = 18) or CD (n = 18) were collected before and during high dose prednisolone treatment (1 mg/kg body weight) and tapering. Friedman's two way analysis of variance, Mann-Whitney U test and Wilcoxon signed-rank sum test were used
Results
Before treatment, plasma from CD patients showed significant elevations in all C-mediated analyses compared to the values obtained from 38 healthy controls (p < 0.02), and in mannan binding lectin (MBL)-concentration and MBL-C4-activation capacity (AC) values compared to UC patients (p < 0.02). Before treatment, plasma from UC patients showed significant elevations only in the classical pathway-mediated C3-AC compared to values obtained from healthy controls (p < 0.01). After treatment was initiated, significant reductions, which persisted during follow-up, were observed in the classical pathway-mediated C3-AC and MBL-C4-AC in plasma from CD patients (p < 0.05).
Conclusion
Our findings indicate that C activation capacity is up-regulated significantly in plasma from CD patients. The decreases observed after prednisolone treatment reflect a general down-regulation in immune activation.
doi:10.1186/1471-230X-5-31
PMCID: PMC1249564  PMID: 16179087

Results 1-4 (4)