The investigation of GSTP1, APC and RASSF1 gene promoter hypermethylation in urine DNA of prostate-diseased patients.

OBJECTIVES: Prostate cancer (PCa) represents one of the most complicated human tumors and, like many others malignancies, arises from progressive genetic and epigenetic alterations. Among all recognized epigenetic alterations, aberrant DNA methylation (hypo- and hypermethylation) is the most important and the best characterized change in PCa. BACKGROUND: We analyzed GSTP1, APC and RASSF1 gene promoter hypermethylation in urine DNA of ten previously non-treated prostate-diseased patients. METHODS: For the purpose, the quantitative real-time methylation specific PCR (MSP) with primers designed for amplification of methylated bisulfite-converted human DNA, followed by melting procedure, was currently optimized. RESULTS: GSTP1 gene promoter hypermethylation was detected in 2 and 1 out of 5 patients with biopsy-confirmed PCa using the primers covering the 3´ and 5´ CpG regions of the promoter, respectively. The APC gene promoter hypermethylation was found in neither of PCa or non-PCa patients and the RASSFI gene promoter hypermethylation was found in some non-PCa and not in all PCa patients. CONCLUSIONS: Our results suggest that GSTP1 gene promoter hypermethylation can be detected in urine DNA of PCa patients with real-time MSP followed by melting. This enables evaluation of its potential as a useful biomarker in the diagnosis and prognosis of PCa (Tab. 1, Fig. 1, Ref. 9).

Variation in CDKAL1 gene is associated with therapeutic response to sulphonylureas.

The aim of the present pilot pharmacogenetic study was to analyse quantitative effects of sulphonylurea treatment in addition to metformin on parameters of glycemic control with respect to CDKAL1 genotypes in patients with type 2 diabetes. Effect of 6-month sulphonylurea therapy on glycemic control according to CDKAL1 genotypes was evaluated in 101 patients with type 2 diabetes who failed to achieve glycemic control on metformin monotherapy. CDKAL1 rs7756992 polymorphism was determined by melting curve analysis of small amplicon following real-time PCR. After sulphonylurea treatment fasting plasma glucose (FPG) levels were significantly different (p=0.045) among three CDKAL1 genotype groups (AA: n=49; AG: n=36; GG: n=16). In a dominant genetic model, carriers of the G-allele (AG+GG, n=52) achieved significantly lower FPG levels in comparison with patients with the AA genotype (6.90±1.08 vs. 7.48±1.12 mmol/l, p=0.013). Consequently, adjusted ΔFPG was significantly higher in the AG+GG compared to the AA group (1.48±1.51 vs. 1.02±1.33 mmol/l, p=0.022). Similar trend was observed for HbA(1c) levels, but the difference between the genotype groups did not reach the level of statistical significance. Relatively small number of included patients is a limitation of the present study. In conclusion, our results suggest that the magnitude of FPG reduction after 6-month sulphonylurea treatment in patients with type 2 diabetes is related to the variation in CDKAL1.

[Relationship of the CDKAL1 and KCNQ1 gene polymorphisms to the age at diagnosis of type 2 diabetes in the Slovakian population]. / Vzt'ah polymorfizmov génov CDKAL1 a KCNQ1 k veku diagnózy diabetu 2. typu v populácii slovenska.

BACKGROUND/AIMS: The association of CDKAL1 and KCNQ1 genes with type 2 diabetes mellitus (DM2T) was confirmed by several genome-wide association studies in both Caucasian and Asian populations. For both genes, it is supposed that the risk of DM2T development is related to impaired insulin secretion. Based on assumption that the presence of risk allele might predispose to an earlier onset of DM2T, the aim of the present study was to assess the frequency of risk alleles of CDKAL1 rs7756992 and KCNQ1 rs163184 polymorphisms and to analyze their association with the age at DM2T diagnosis in the Slovakian population. METHODS: CDKAL1 rs7756992 A/G and KCNQ1 rs163184 G/T polymorphisms were genotyped using asymmetric PCR with subsequent melting curve analysis in a group of 538 patients with DM2T. Anthropometric and laboratory parameters were determined by using standard methods. Since two genes were analysed, the required level for statistical significance was defined as p < 0.025. RESULTS: Risk homozygotes (CG) for KCNQ1 polymorphism had higher mean age of DM2T diagnosis by 2 years when compared to T-allele carriers (GT + TT) in a recessive model, but the difference did not reach the predefined level of statistical significance. No relationship of CDKAL1 polymorphism to the age at onset of DM2T diagnosis was observed. CONCLUSIONS: In the present study, no relationship of CDKAL1 and KCNQ1 polymorphisms to the earlier onset of type 2 diabetes was observed.

Epigenetic studies in human diseases.

Irreversible genetic alterations underlying human diseases have been widely studied to date. However, it is evident that the potentially reversible epigenetic dysregulations may also have an important role in the disease origin. The studies of epigenetic mechanisms underlying disease onset, progression and pathogenesis have been performed in various human disorders. The epigenetic approaches may reveal useful markers for disease diagnostics, classification and prognostics as well as for progressive pharmacological treatment. This review summarizes the studies of epigenetic dysregulations including aberrant methylation, histone modifications and miRNA alterations in cancer as well as the studies of methylation changes and aberrant histone modifications in neurodegenerative, autoimmune, cardiovascular and other diseases. The imprinting disorders together with the emerging role of epigenetics in nutritional genomics, environment-organism interaction studies and in some other fields are also mentioned.

Relationship of five type 2 diabetes candidate gene polymorphisms to the age at diagnosis of diabetes in the Slovakian population.

OBJECTIVES: To examine the relationship between polymorphisms of five candidate genes for type 2 diabetes mellitus (T2DM) and the age at diagnosis of T2DM. METHODS: 538 Slovakian patients with T2DM were included and their age at diagnosis of T2DM retrieved from their medical records. Polymorphisms of genes encoding peroxisome proliferator activated receptor gamma (PPARG), PPARG-coactivator-1 (PGC1), insulin-receptor substrate 1 (IRS1), the subunit Kir 6.2 of the ATP-dependent potassium-channel (KCNJ11) and transcription factor 7-like 2 (TCF7L2) were detected by PCR-RFLP methods. RESULTS: No significant relationship between the risk alleles of the examined gene polymorphisms to the lower mean age at diagnosis of T2DM was observed. The carriers of the TT-genotype of TCF7L2 rs7903146 polymorphism had significantly increased odds ratio for diagnosis of diabetes before the age of 40 years [OR 3.02 (1.34, 6.81), p = 0.008], in comparison with the CC/CT genotype carriers. CONCLUSION: No significant association of PPARG, PGC1, IRS1, KCNJ11 and TCF7L2 gene polymorphisms and the age at diagnosis of T2DM was observed in the present study. Homozygotes for the risk allele of TCF7L2 had more frequently early onset of T2DM, before age of 40 years (Tab. 4, Ref. 15).

New evidence for the synteny of rice chromosome 1 and barley chromosome 3H from rice expressed sequence tags.

To provide improved access to the wealth of resources and genomic information that is presently being developed for rice a set of 88 rice expressed sequence tags (ESTs) previously mapped on rice chromosome I in the cross 'Nipponbare' x 'Kasalath' was used for comparative mapping in a cross of the barley cultivars 'Igri' and 'Franka'. As expected. most (89%) of the clones gave distinct banding patterns in barley of which about one-third was polymorphic between 'Igri' and 'Franka'. These polymorphisms were mapped, and most of these (56%) confirmed that rice chromosome 1 and barley chromosome 3H are syntenous. All single-copy markers identified conserved collinear positions, while markers with multiple copies did so in a few cases only. The markers that were not fitting in the collinear order were distributed randomly across the barley genome. The comparative maps of barley chromosome 3H and rice chromosome 1 comprise in total 26 common markers covering more than 95% of the genetic length of both chromosomes. A 30-fold reduction of recombination is seen around the barley centromere, and synteny may be interrupted in this region. However, the good overall synteny on a mesoscale (1-10 cM) justifies the use of rice as a platform for map-based cloning in barley.