Zita Aušrelė Kučinskienė

Genetic Variants in COL2A1, COL11A2, and IRF6 Contribute Risk to Nonsyndromic Cleft Palate

BACKGROUND Orofacial clefts are among the most common birth defects with a strong genetic component. Nonsyndromic cleft palate (NSCP) is a complex malformation determined by the interaction between multiple genes and environmental risk factors. METHODS We conducted a case-control association study to investigate the role of 40 candidate genes in predisposition to orofacial clefting. Five hundred ninety-one haplotype tagging single nucleotide polymorphism (tagSNPs) were genotyped in a clefting sample from the Baltic region, composed of 104 patients with nonsyndromic cleft palate and 606 controls from an Estonian, Latvian, and Lithuanian population. RESULTS In case-control comparisons, the minor alleles of IRF6 rs17389541 (p = 5.45 × 10(-4)) and COL2A1 rs1793949 (p = 7.26 × 10(-4)) were associated with increased risk of NSCP. Multiple haplotypes in COL2A1 and COL11A2 and haplotypes in WNT3, FGFR1, and CLPTM1were associated with NSCP. The strongest associations were found for IRF6 haplotype rs17389541/rs9430018 GT (p = 2.23 × 10(-4)) and COL2A1 haplotype rs12822608/rs6823 GC (p = 3.68 × 10(-4)). The strongest epistatic interactions were observed between MSX1 and BMP2, FGF1 and PVRL2, and COL2A1 and FGF2 genes. CONCLUSIONS This study provides for the first time evidence of the implication of IRF6, COL2A1, and WNT3 in the occurrence of NSCP. It is likely that variation in cartilage collagen II and XI genes, IRF6, and the Wnt and FGF signaling pathway genes contributes susceptibility to nonsyndromic cleft palate in Northeastern European populations.

De novo 5q35.5 duplication with clinical presentation of Sotos syndrome

We report on a girl with developmental delay and a de novo 264 kb interstitial duplication in the region of Sotos syndrome at 5q35.3 in the immediate vicinity of critical NSD1 gene, but manifesting the phenotype, of overgrowth both prenatal stage and postnatal, macrocephaly, developmental delay, and resembling that of Sotos syndrome, rather than the recently reported syndrome of reciprocal duplication. The duplication is located right downstream from the NSD1 gene, a region which appears critical for the expression of the gene as regulatory elements might be disrupted or the expression of a not amplified critical gene might be otherwise affected by the duplicated region. Thus, in the process of evaluating identified CNVs attention should be drawn to the possible influence of chromosomal rearrangement on distant genes, which could add additional diversity to genomic disorders. Our case demonstrates that evaluation of the size of chromosomal alteration and gene content are not sufficient for assessment of CNVs pathogenicity and the context of adjacent genes should be considered.

Combined studies of chemical composition of urine sediments and kidney stones by means of infrared microspectroscopy

Abstract. Results of the structural analysis of urinary sediments by means of infrared spectral microscopy are presented. The results are in good agreement with the results of standard optical microscopy in the case of single-component and crystalline urinary sediments. It is found that for noncrystalline or multicomponent sediments, the suggested spectroscopic method is superior to optical microscopy. The chemical structure of sediments of any molecular origin can be elucidated by this spectroscopic method. The method is sensitive enough to identify solid particles of drugs present in urine. Sulfamethoxazole and traces of other medicines are revealed in this study among the other sediments. We also show that a rather good correlation exists between the type of urinary sediments and the renal stones removed from the same patient. Spectroscopic studies of urinary stones and corresponding sediments from 76 patients suffering from renal stone disease reveal that in 73% of cases such correlation exists. This finding is a strong argument for the use of infrared spectral microscopy to prevent kidney stone disease because stones can be found in an early stage of formation by using the nonintrusive spectroscopic investigation of urinary sediments. Some medical recommendations concerning the overdosing of certain pharmaceuticals can also be derived from the spectroscopic studies of urinary sediments.

Classical rather than genetic risk factors account for high cardiovascular disease prevalence in Lithuania: A cross-sectional population study

PURPOSE Cardiovascular disease (CVD) mortality accounts for 54% of all deaths in Lithuania, making it the highest among all of the European Union countries. We evaluated the prevalence of several CVD risk factors, including lifestyle, blood biochemistry and genetic predisposition to determine the reasons behind significantly increased CVD prevalence in Lithuania. MATERIALS AND METHODS In total 435 volunteers of Lithuanian ethnicity and stable geographic settlement for 3 generations, had their anthropometric, biochemical and behavioural risk factors measured. A randomly selected sample of 166 volunteers had their 60 CVD risk alleles genotyped. The prevalence of risk alleles and cumulative CVD genetic risk score were compared with population of North-West European origin (CEU) using data from the phase 3 HapMap project. RESULTS CVD was present in 33.8% of study volunteers, 84% of participants consumed alcohol, 21% were current smokers and only 30% of participants engaged in higher levels of physical activity. Also, the average BMI (males 28.3±4.3kg/m2, females 27.3±5.0kg/m2), total cholesterol (males 6.1±1.2mmol/L, females 6.2±1.0mmol/L) and LDL-cholesterol (males 4.1±1.1mmol/L, females 4.1±1.0mmol/L) were above the normal values. The cumulative genetic susceptibility to develop CVD in Lithuanians was only 1.4% higher than in CEU population. CONCLUSIONS High BMI and poor population plasma lipid profile are the major contributing factors to high CVD mortality and morbidity in Lithuania. Smoking, alcohol consumption and preliminary genetic predisposition results do not explain the difference in CVD mortality between the Lithuanian and wider European populations. CVD prevention programmes in Lithuania should primarily focus on weight loss and improving blood lipid control.

Monitoring of T-cell acute lymphoblastic leukemia by flow cytometry

Minimal residual disease (MRD) predicts the outcome of acute lymphoblastic leukemia (ALL). Flow cytometry (FC) is one of the most sensitive and most applicable methods for MRD diagnostics, but there is still no agreement on the “gold standard” of the method. We tried to optimize flow cytometric MRD detection in T-ALL. Fourteen adults and 11 children with T-ALL and 12 normal bone marrow (BM) donors were enrolled in the study. We found that the most common phenotypic aberrations in T-ALL were TdT and CD99 coexpression on T-cells in BM. Therefore for MRD detection we developed a limited four-color marker panel (TdT/CD7/cCD3/CD19 and CD99/CD7/cCD3/CD2) and a standard analysis strategy. This assay was evaluated on BM of healthy controls. Less than 0.01% TdT+ or CD99 bright T-cells were found in normal BM. MRD was detected in 9 adult patients and 1 child at different time-points of treatment. The average TdT and CD99 mean fluorescence intensity (MFI) value of residual blasts fluctuated during therapy, but it still remained higher than MFI of normal T-cells. Our established MRD detection method differentiated leukemic lymphoblasts with sensitivity in the range of 0.01% and did not give any false positive results in normal BM.

Prevalence of Metabolic Syndrome in Patients with Uric Acid and Calcium–based Kidney Stones

The aim of the study was to investigate the prevalence of metabolic syndrome in patients with uric acid and calcium–based kidney stones and to investigate the relationship between metabolic syndrome and type of kidney stone using infrared spectroscopy to evaluate the chemical composition of kidney stones Sixty patients with urolithiasis were examined. Metabolic syndrome was diagnosed according to clinical and laboratory criteria. Weight, height, body mass index, waist circumference, and blood pressure of patients were measured. Blood tests were performed. Concentrations of total cholesterol, low density lipoprotein cholesterol, high density lipoprotein cholesterol, triglycerides, glucose and uric acid in blood, were analyzed. The kidney stones of patients were removed and the composition of each kidney stone was analyzed using Fourier transform infrared spectroscopy. Metabolic syndrome was diagnosed in 55% of the patients; 86.7% of patients with uric acid (UA) kidney stones and 44.4% of patients with calcium (Ca) based stones had metabolic syndrome. All patients diagnosed with metabolic syndrome were overweight or obese. Even though there were no statistically significant differences observed concerning the anthropometrical measures and arterial blood pressure (BP) between the UA stone formers and Ca–based stone formers, the results show a trend that failed to reach significance: higher waist size, BMI and arterial BP means in the group of patients with UA stones than in the patients with Ca–based stones. No statistically significant differences in lipid profile between the groups were found. Concentration of UA in blood serum was significantly higher in patients with UA kidney stones than it was in patients with Ca–based kidney stones. Significant positive correlation between triglycerides and serum UA concentrations, as well as body mass index and serum UA concentration, and negative correlation between concentrations of high-density lipoprotein cholesterol and UA was found. Conclusion: Metabolic syndrome was more prevalent in patients with uric acid stones than in the patients with calcium–based kidney stones, even though this relationship was not statistically significant, most likely because of the limited number of patients investigated.