AA Variants Research Articles

Prognostic model for the development of cardiomyopathies based on genetic predictors

Aim. To develop a prognostic model for the development of primary and secondary cardiomyopathy based on genetic predictors.Material and methods. The study included 221 patients with cardiomyopathy. The mean age of the participants was 55,30±9,69 years, with the age range from 20 to 77 years. Two following groups of patients were determined: the first group (n=111) with idiopathic dilated cardiomyopathy (DCM) and the second group (n=110) with ischemic myocardial dilation. DNA was extracted from the venous blood of all participants using phenol-chloroform extraction for subsequent genotyping using polymerase chain reaction and restriction fragment length polymorphism analysis.Results. The performed multivariate analysis using the stepwise selection method showed a significant effect of the following predictors at the third step: AG/GG allelic variant of the SCN5A gene (rs1805124), 6a/6a allelic variant of the MMP3 gene (rs35068180) and the patient's age.The performed multivariate analysis using the stepwise selection showed a significant effect of the following predictors: AG/GG allelic variant of the CTLA4 gene (rs231775), AA and AG allelic variants of the SCN5A gene (rs1805124).Conclusion. Genetic studies on cardiomyopathies reveal significant associations between certain single nucleotide polymorphisms and the risk of disease development. The study results showed that the AG/GG allelic variant of the SCN5A gene (rs1805124), 6a/6a allelic variant of the MMP3 gene (rs35068180) and the patient's age have prognostic significance in the development of DCM. In addition, AG/GG allelic variant of the CTLA4 gene (rs231775), AA and AG allelic variants of the SCN5A gene (rs1805124) have prognostic significance in the development of ischemic myocardial dilation.

POLYMORPHISM OF GENES RESPONSIBLE FOR NEUROHUMORAL MECHANISMS OF DEVELOPMENT OF CHRONIC HEART FAILURE WITH PRESERVED EJECTION FRACTION IN PERSONS WITH TYPE 2 DIABETES MELLITUS

The search for genetic markers of chronic heart failure (CHF), comorbid with type II diabetes mellitus, is an urgent task. The study aim was to identify genetic polymorphisms associated with impaired neurohumoral regulation in patients with CHF with preserved and low ejection fraction and type II diabetes mellitus. Material and methods. Polymorphisms of genes responsible for neurohumoral mechanisms of CHF development were studied in 167 patients (69.9±10.1 years) with type II diabetes mellitus, hypertension, CHF with preserved or low ejection fraction, and healthy volunteers. Results and discussion. The angiotensin gene, angiotensin-converting enzyme, angiotensin 1 and 2 receptors polymorphisms are not involved in the CHF formation in patients with type II diabetes mellitus. In the control group, rs1403543 GA polymorphism was found in 90.48% of the examined, in patients with CHF with preserved ejection fraction and type II diabetes mellitus, GA and AA variants were found in 20% of cases, in the CHF group with a low ejection fraction AA polymorphism was found in 53.85% of the examined. It is possible they do not participate in the formation of CHF in patients with type II diabetes mellitus, or have a protective effect. The gene GNB: 825 C > T rs5443 polymorphism was detected from 53.33 to 61.9% of the examined in all groups. rs1799998 polymorphism is not associated with the development of CHF. The rs2070744 polymorphism is associated with the development of CHF with a preserved ejection fraction, but not CHF with a low ejection fraction, in patients with type II diabetes mellitus. The gene NOS3: 894 G > T rs1799983 in heterozygous and homozygous variants polymorphism was more common in patients with CHF with preserved ejection fraction (statistically insignificant). Conclusions. CHF with a preserved ejection fraction and CHF with a low ejection fraction in patients with type II diabetes mellitus are associated with different polymorphisms and have different pathogenesis. The gene AGTR2 polymorphism rs1403543 in patients with type II diabetes mellitus and CHF with preserved ejection fraction occurs less frequently than in the control group. The gene GNB polymorphism rs5443 in patients with CHF with a preserved ejection fraction and CHF with a low ejection fraction occurs much less frequently than in the control group. The gene NOS3 polymorphism rs2070744 in patients with CHF with a preserved ejection fraction occurs significantly more often than in the control group and in patients with CHF with a low ejection fraction.

Effects of leptin and thyroglobulin gene polymorphisms on beef colour in Holstein bulls for slaughter in Turkey

n the present work, live weight (LW), hot carcass weight (HCW), and beef colour values of Turkish Holstein bull (THBs) samples, and their relationship with single nucleotide polymorphisms (SNPs) variants were determined. E2JW and E2FB variants of leptin (LEP), and C422T variant of thyroglobulin (TG) genes were determined in 100 heads of THBs by polymerase chain reaction fragment length polymorphism (PCR-RFLP). Genotyping was carried out by capillary electrophoresis. The colour of raw and cooked beefs was spectrophotometrically measured before and after cooking. The cooked beefs were significantly brighter in the LEP E2JW AA and AT variants than in the TT genotype (p < 0.05). Based on b* of raw beefs, the yellowish colour density in the LEP E2JW AA genotype variant was significantly higher than in AT and TT (p < 0.05). The most significant correlation was determined between b* and L* (0.695), and b* and a* (0.694) of raw beefs, while the correlation coefficient between LW and HCW was found to be 0.604 (p < 0.01). The LEP E2JW AA marker genotype for cattle with brighter and more intense beef, and the LEP E2JW TT variant genotype to increase beef yield should be selected as a study by using MAS method at an early age. Also, AT / CT / CC marker genotypes of THBs should be selected in LEP E2JW / E2FB / TG C422T marker loci, respectively to generate more income from the increase in LW and HCW.

A comprehensive analysis of the mutational landscape of the newly emerging Omicron (B.1.1.529) variant and comparison of mutations with VOCs and VOIs.

The Omicron variant is spreading rapidly throughout several countries. Thus, we comprehensively analyzed Omicron’s mutational landscape and compared mutations with VOC/VOI. We analyzed SNVs throughout the genome, and AA variants (NSP and SP) in VOC/VOI, including Omicron. We generated heat maps to illustrate the AA variants with high mutation prevalence (> 75% frequency) of Omicron, which demonstrated eight mutations with > 90% prevalence in ORF1a and 29 mutations with > 75% prevalence in S-glycoprotein. A scatter plot for Omicron and VOC/VOI’s cluster evaluation was computed. We performed a risk analysis of the antibody-binding risk among four mutations (L452, F490, P681, D614) and observed three mutations (L452R, F490S, D614G) destabilized antibody interactions. Our comparative study evaluated the properties of 28 emerging mutations of the S-glycoprotein of Omicron, and the ΔΔG values. Our results showed K417N with minimum and Q954H with maximum ΔΔG value. Furthermore, six important RBD mutations (G339D, S371L, N440K, G446S, T478K, Q498R) were chosen for comprehensive analysis for stabilizing/destabilizing properties and molecular flexibility. The G339D, S371L, N440K, and T478K were noted as stable mutations with 0.019 kcal/mol, 0.127 kcal/mol, 0.064 kcal/mol, and 1.009 kcal/mol. While, G446S and Q498R mutations showed destabilizing results. Simultaneously, among six RBD mutations, G339D, G446S, and Q498R mutations increased the molecular flexibility of S-glycoprotein. This study depicts the comparative mutational pattern of Omicron and other VOC/VOI, which will help researchers to design and deploy novel vaccines and therapeutic antibodies to fight against VOC/VOI, including Omicron.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11357-022-00631-2.

Rasagiline Pharmacokinetics in CYP1A2 Variant Healthy Smokers & Non-smokers in Different Doses.

Objectives:Rasagiline, a drug for Parkinson’s disease is metabolized by CYP1A2 enzyme. The objective of the study was to investigate the influence of cytochrome P450 1A2 variants and smoking status of healthy individuals on the pharmacokinetics of rasagiline.Methods:A comparative, open label, interventional, single oral dose, pharmacokinetic study was performed on 108 healthy volunteers in UHS & UVAS, Lahore. Data collection was initiated in June 2016 and ended in January 2018. It was divided in three phases with 1, 2 and 5mg of rasagiline given to a group of 36 volunteers in each phase. Volunteers were sub-divided into six groups of AA smokers, AA non-smokers, AC smokers, AC non-smokers, CC smokers & CC non-smokers on the basis of genotyping and smoking status. Serial blood sampling was performed at 0, 0.25, 0.5, 0.75, 1, 1.5, 2, 3, 4, 6, 8 & 12 hours after administration of rasagiline tablets. Plasma concentrations were determined using High Performance Liquid Chromatography (HPLC) method. Pharmacokinetic (PK) parameters were calculated using software (APO) pharmacological analysis.Results:Analysis of variance (ANOVA) showed significant difference between AA and CC groups. Multiple group comparison with post hoc Tukey’s revealed that AA-smokers had significantly less tmax (p<0.001), t1/2 (p<0.012), AUC (p<0.008) and highest Cl (p<0.001) as compared to CC-smokers. The trend was same across all three doses.Conclusion:The study concludes that the systemic metabolism of rasagiline is significantly increased in CYP1A2*AA variants while smoking status did not show consistent difference in PK parameters.

Assessment of Methaemoglobin in Haemoglobin Variants in Selected Ethnic Groups in Bayelsa State

Methaemoglobin (Met-Hb) is a type of the oxygen-carrying metalloproteinhemoglobin. The heme group iron exists as ferric (Fe3+) iron, rather than the ferrous (Fe2+) iron of typical hemoglobin. Met-Hb is unable to perform the function of binding to oxygen like oxyhaemoglobin does. The aim of this study was to compare methaemoglobin levels between AA and AS haemoglobin variants among the Ijaw, Igbo and Yoruba ethnic groups residing in Bayelsa State, Nigeria. A total of 150 subjects were enrolled for the study. One hundred and sixteen subjects constituted the Ijaws; 21 Igbos and 13 Yorubas. For each subject, 4mls of blood sample collected in EDTA bottle was assayed for methaemoglobin using a spectrophotometric method. Results revealed there was no significant difference in the methaemoglobin mean levels between the AA and AS haemoglobin variants (P-value&gt;0.05) of the ethnic groups except the Igbo ethnic group (P-value &lt;0.05). However, comparing the methaemoglobin mean levels among the ethnic groups showed a significant mean difference of methaemoglobin (P-value &lt;0.05). All Post-hoc groups showed significant difference except the Igbo and Yorubo ethnic groups (P-value &gt;0.05). In conclusion, this study has revealed that methaemoglobin levels changes significantly based on studied tribes but does not change based on studied haemoglobin variants.

HIF-1α and VEGF polymorphisms and systemic lupus erythematosus susceptibility

BackgroundHypoxia-inducible factor-1α (HIF-1α) and its downstream gene, vascular endothelial factor (VEGF), play an important role in modulating the immune system function and consequently alternation the susceptibility to systemic lupus erythematosus (SLE) disease. ObjectiveThe present study aimed to investigate the effect of the HIF-1α and VEGF gene polymorphisms and the susceptibility to SLE. MethodsThe 140 patients and 150 healthy age and gender-matched people as a control group participated in the study. The PCR-RFLP method was used for genotyping. ResultsNo remarkable differences in allele frequencies of HIF-1α (rs11549465) and VEGF (rs699947) were seen between the SLE and control groups. The frequencies of CT genotype of the HIF-1α (rs11549465) and CA genotype of VEGF (rs699947) in the control were significantly higher than SLE group (OR = 0.53; 95% CI = 0.32–0.53; p = 0.014; OR = 0.57;95% CI = 0.33–0.99; p = 0.046, resp.). In the case of HIF-1α (C111A) polymorphism, the CA and AA variants were not found. ConclusionHIF-1α (rs11549465) CT and VEGF (rs699947) CA genotypes were identified as protective factors for SLE. However, additional studies are required to confirm the association between HIF-1α and VEGF polymorphisms and SLE.

Il-18 Overproduction Associated with NLRP1 Single Nucleotide Polymorphisms Linked to Risk for Vitiligo

Background The NLRP1gene is central to the NLR inflammasome. Variants to the NLRP1 gene are associated with vitiligo and other autoimmune diseases. We examined the effects of two single nucleotide polymorphisms (SNP) son cytokine levels and NLRP1 gene expression in 50 human volunteers. Methods NLRP1 was genotyped at SNPs rs2670660 and rs12150220, and participants who were homozygous at one or more SNP were analyzed. Plasma IL-18 and IL-1β levels were quantified using ELISA. NLRP1 gene expression was measured using real-time PCR. Results Participants with the risk genotype had significantly higher levels of plasma IL-18 than participants with protective genotype (0.439 ng/µL compared to 0.152 ng/µL, p = 0.024). Genotypes rs2670660 and rs12150220 were strongly linked in this population (p = 2.33 x 10-13). Conclusions Increased production of IL-18, suggests that at least one of the AA variants of rs2670660 or rs12150220 increases NLRP1 activity. rs2670660 and rs12150220 are strongly linked.

Leptin, Galectin-3 and Angiotensin II Type 1 Receptor Polymorphism in Overweight and Obese Patients with Heart Failure – Role and Functional Interplay

Background and AimsLeptin, one of the best-known adipocytes, together with the renin-angiotensin-aldosterone system and galectin-3 are important players in inflammation, arterial hypertension and heart failure pathophysiology. Moreover, uninucleotide A1166C polymorphism is associated with hypertension and poor prognosis in heart failure. The aim of the study was to investigate a possible relationship between leptin serum values, specific heart failure biomarkers and the presence of AT1 receptor A1166C polymorphism in overweight and obese heart failure patients.MethodsThe study included 88 consecutive overweight and obese patients admitted for decompensated heart failure. NT-proBNP, MR-proANP, galectin-3 and leptin levels were determined on the arrival day. Genotyping of the A1166C allele – AT1 receptor gene was performed in all patients in order to find variants.ResultsWe found a strong positive correlation (r = 0.347, p = 0.001) between leptin serum concentrations and BMI. Leptin levels were not correlated with heart failure biomarkers (NT-proBNP, MR-proANP and galectin-3). All homozygote CC variants were hypertensive, but we registered no significant difference in genetic AC and AA variants distribution between hypertensive and normotensive. Leptin was not significantly modified by the presence of potentially pathogenic A1166C–AT 1 receptor genotypes (AC + CC). But, galectin-3 was found in higher concentrations in patients with heterozygous and homozygous A1166C mutations.ConclusionOverweight and obese patients with heart failure display high leptin serum levels. Leptin does not offer incremental prognostic value in heart failure overweight and obese patients. But, galectin-3 was found in higher concentrations in patients with heterozygous and homozygous A1166C mutations, suggesting a worse prognosis probably due to more advanced cardiac fibrosis.

Association of single nucleotide polymorphisms in the somatotropin gene with indicators of meat productivity in meat-wool sheep

Modern methods, which are based on the use of DNA technology, allow scientists to improve the accuracy and efficiency of traditional breeding by using molecular markers. One of the ways to identify markers is DNA assessment in the candidate gene, which is the basis of the trait and contributes to the manifestation of the phenotypic characteristics of the organism. Currently, there is growing interest in the genetic improvement of economically important traits in sheep [Fatima Abd Al-Muhsen et al., 2019]. The study of the relationship between gene polymorphism and productivity indicators has high practical importance, which lies in solving many applied problems of breeding. One of these tasks is to determine genetic markers which affect the meat productivity of sheep [Serdyuk G.N., Prituzhalova A.O., 2019; Pogodaev V.A., Kononova L.V., et al., 2019; Lushnikov V.P., Fetisova T.O., Selionova M.I. et al., 2020]. Growth hormone gene GH, which controls and regulates the growth and development of animals, can be considered as a promising marker gene for evaluating meat productivity. The study focuses on the research of the somatotropin gene polymorphism and the analysis of its associations with the indicators of meat productivity of meat-wool sheep of the genotype 1/2 Poll Dorset x 1/2 North Caucasian meat-wool (1/2 PD х 1/2 SC), which are bred in the Stavropol Territory. Polymorphism of somatotropin gene loci was carried out by polymerase chain reaction (PCR) followed by the determination of the restriction fragments lengths – RFLP. The results of PCR showed that the polymorphism of somatotropin gene is represented by two alleles A and B. When studying the polymorphism of GH gene in the experimental animals, genotypes AA, BB and AB were found with different frequency of occurrence. It was found that the heterozygous AB genotype (42.8%) was the most common in meat-wool sheep, while the homozygous AA and BB variants were basically equal and amounted to 29.7 and 27.5%. Further research made it possible to analyze the relationship of the allelic variants of the somatotropin gene with the slaughter parameters of meat-wool sheep. Based on the results, we found that the presence of heterozygous AB and homozygous BB genotypes has a positive effect on the indicators of sheep meat productivity.

Association of genetic variants of RNF213 with ischemic stroke risk in Koreans.

Large artery disease (LAD), cardioembolism (CE), and small vessel disease (SVD) are well-established causes of ischemic stroke. Although a founder variant of RNF213 has been regarded a genetic susceptibility for Moyamoya disease (MMD) and certain types of intracranial atherosclerotic stenosis (ICAS), correlations between RNF213 variants and ischemic stroke with SVD remain largely unknown. This study aimed to characterize the associations of four RNF213 polymorphisms (4448G>A, 4810G>A, 4863G>A, and 4950G>A) with ischemic stroke subtypes in Koreans. Genetic data from 529 stroke patients were analyzed and compared to 424 age- and sex-matched controls. Genetic variants of RNF213, as obtained from the Human Gene Mutation Database, were analyzed in the study subjects using the polymerase chain reaction restriction fragment length polymorphism assay. We investigated four single-nucleotide polymorphisms of RNF213 to elucidate their association with ischemic stroke [LAD, (n = 192), SVD (n = 145) and CE (n = 51)]. The RNF213 4950G>A genotype was observed more frequently in cerebral stroke patients and was more strongly associated with SVD than LAD (P = 0.014). RNF213 4448/4950 in combination with G-A was higher in SVD patients. However, the RNF213 4863/4950 allele combination was associated with increased risk of SVD and LAD. These results confirmed that RNF213 4950GA+AA variants were more frequent in ischemic stroke, especially in SVD, and that RNF213 G-G-G-A and G-G-G-A (4448/4810/4863/4950) haplotype sequences play a role in LAD and CE as well as SVD. Our data reported that theRNF2134950G>A genotypes and severalRNF213(4448/4810/4863/4950) haplotypes were associated with ischemic stroke in Koreans.

Can the FUT 2 Gene Variant Have an Effect on the Body Weight of Patients Undergoing Bariatric Surgery?—Preliminary, Exploratory Study

Background: The FUT2 gene (Se gene) encoding the enzyme α-1,2-L-fucosyltransferase 2 seems to have a significant effect on the number and type of bacteria colonizing the intestines. Methods: In a group of 19 patients after bariatric surgery, the polymorphism (rs601338) of FUT2 gene was analyzed in combination with body mass reduction, intestinal microbiome (16S RNA sequencing), and short chain fatty acids (SCFA) measurements in stools. Results: Among the secretors (Se/Se polymorphism of the FUT2 gene rs601338, carriers of GG variant), correlations between waist-hip ratio (WHR) and propionate content and an increase in Prevotella, Escherichia, Shigella, and Bacteroides were observed. On the other hand—in non-secretors (carriers of GA and AA variants)—higher abundance of Enterobacteriaceae, Ruminococcaceae, Enterobacteriaceae, Clostridiales was recorded. Conclusions: The increased concentrations of propionate observed among the GG variants of FUT 2 may be used as an additional source of energy for the patient and may have a higher risk of increasing the WHR than carriers of the other variants (GA and AA).

Searching for Predictors of Migraine Chronification: a Pilot Study of 1911A>G Polymorphism of TRPV1 Gene in Episodic Versus Chronic Migraine.

Transient receptor potential vanilloid type 1 (TRPV1) receptors activated by heat and capsaicin are expressed in trigeminal nociceptive neurons and implicated in the generation of migraine pain. Genetic studies suggested that single-nucleotide polymorphism (SNP) 1911A>G (rs8065080), leading to amino acid substitution Ile585Val, in the TRPV1 gene affects functional activity of TRPV1 receptors and is involved in different pain conditions. However, this polymorphism has not been tested in migraine patients. The objective of this pilot study was to investigate genetic factors of migraine susceptibility. We evaluated frequency distribution of AA, AG, and GG variants of SNP 1911A>G in the TRPV1 gene in patients with episodic and chronic migraine compared with healthy individuals. The study included 46 patients diagnosed with migraine (27 episodic and 19 chronic) and 50 healthy individuals as a control group. DNA from peripheral blood was used to test TRPV1 SNP using allele-specific PCR combined with gel electrophoresis. The genotype frequency distribution in episodic migraine was comparable with that in controls (AA 33%, AG 56%, GG 11% and AA 34%, AG 46%, GG 20%, respectively). On the contrary, in chronic migraine, the distribution differed significantly (p < 0.05) (AA 68%, AG 32%, GG 0%). This are first indications for a distinctive genotype frequency distribution of TRPV1 1911A>G in chronic migraine patients compared with episodic migraine patients and controls. Our data confirm a different predisposition to chronic pain in migraine and give a prerequisite for a new look at the nature of chronification of migraine, proposing that the absence of GG genotype may be considered as possible risk biomarker of episodic migraine evolution to chronic form.

Inheritance of allelic variants of the kappa-casein gene by cows

The inheritance of allelic variants of the kappa-casein gene from bulls with different genotypes and their influence on the milk production of daughters were studied. For research, PCR diagnostics of daughters in the herds of black-and-white cattle at the farms “Azeleevo” and “Vakhitovo” (OJSC “Red East Agro”) was carried out, the fathers were two bulls LADDIE 135797213 with a genotypes CSN3 AB and LOMAX 10785322 with a genotype CSN3 BB. Based on the results of genotyping, the frequency of occurrence of genotypes AA, AB, BB kappa-casein and allelic variants A and B in daughters was calculated. The bull with the CSN3 AB genotype produced the largest number of offspring with the CSN3 AA genotype 50.0-51.8 %, and the bull with the homozygous BB genotype produced 24–25 % of daughters carrying the BB variant and 75 -76 % of the AB genotype. The frequency of occurrence of the Kappa-casein allele in the daughters of bulls with the genotype CSN3 BB was 0.63, which is almost 2 times more than the allele A. When comparing heifers with the same genotype (CSN3 AB), it was found that at the Azeleevo farm, the daughters of the bulls having the genotype BB of kappa-casein are superior to cows born from bulls with the genotype AB by the milk yield (+36 kg), mass fraction of fat and protein (+0.01 %), the amount of milk fat (+2 kg) and protein (+2 kg). In the group of first-calf heifers with the BB genotype, daughters of the producer with the BB genotype are superior by the milk yield (+ 175 kg), the mass fraction of fat in milk (+0.1 %), the amount of milk fat (+12 kg), the mass fraction of protein in milk (+0.09 %), the amount of milk protein (+11 kg). At the Vakhitovo farm, similar results in the group of CSN3 AB heifers born from the bulls with the BB genotype was observed

Association of MLH1 single nucleotide polymorphisms with clinical outcomes of first-line irinotecan-based chemotherapy in colorectal cancer.

PurposeSeveral studies have proved that single nucleotide polymorphisms (SNPs) of mismatch repair system genes are closely related to the development of colorectal cancer (CRC) by causing microsatellite instability, while effects of the SNPs of MMR system-related genes on the clinical outcomes of cytotoxic chemotherapy are less understood. The aim of this study explored the influence of MLH1 SNPs on clinical outcomes of first-line irinotecan-based chemotherapy in CRC.Patients and methodsA total of 125 metastatic colorectal cancer (mCRC) patients who received first-line irinotecan-based chemotherapy (none of them combined with bevacizumab or cetuximab) were enrolled in this study. Blood samples or formalin-fixed paraffin-embedded tissues of study population were taken. DNA isolation and genotyping analyzed were obtained for potential functional polymorphisms of MLH1 rs1800734 by real-time PCR. Progression-free survival (PFS) was the primary endpoint and tumor response rate (RR) was the secondary endpoint of this study.ResultsOf all the assessable population, the result showed no statistical difference among the three types SNPs of MLH1 rs1800734 (AA, AG, GG) for RR (P=0.859), and also without significant difference for AA + AG combined variants vs GG variant (P=0.849). The median PFS for AA, AG, and GG variants of MLH1 rs1800734 SNPs were 9.4 months, 7.0 months, and 6.9 months, respectively (log-rank P=0.031). Interestingly, compared with AA variant of MLH1 rs1800734 SNPs, GG variant showed a shorter PFS (HR: 3.49; 95 CI: 1.02–11.94; P=0.046). Furthermore, the median PFS of AA + AG combined variants and GG variant were 8.3 months and 6.9 months (log-rank P=0.037), and GG variant have a decreased trend with no significant difference (HR: 1.57; 95 CI: 0.98–2.53; P=0.061).ConclusionThe AA variant of MLH1 rs1800734 SNPs has a longer PFS in first-line irinotecan-based chemotherapy for mCRC patients, and the result needs to be further confirmed by prospective studies in the future.

In Silico Analysis of Hepatitis B Virus Occult Associated Mutations in Botswana Using a Novel Algorithm.

Occult hepatitis B infections (OBI) represent a reservoir of undiagnosed and untreated hepatitis B virus (HBV), hence the need to identify mutations that lead to this phenotype. Functionally characterizing these mutations by in vitro studies is time-consuming and expensive. To bridge this gap, in silico approaches, which predict the effect of amino acid (aa) variants on HBV protein function, are necessary. We developed an algorithm for determining the relevance of OBI-associated mutations using in silico approaches. A 3 kb fragment of subgenotypes A1 and D3 from 24 chronic HBV-infected (CHB) and 24 OBI participants was analyzed. To develop and validate the algorithm, the effects of 68 previously characterized occult-associated mutations were determined using three computational tools: PolyPhen2, SNAP2, and PROVEAN. The percentage of deleterious mutations (with impact on protein function) predicted were 52 (76.5%) by PolyPhen2, 55 (80.9%) by SNAP2, and 65 (95.6%) by PROVEAN. At least two tools correctly predicted 59 (86.8%) mutations as deleterious. To identify OBI-associated mutations exclusive to Botswana, study sequences were compared to CHB sequences from GenBank. Of the 43 OBI-associated mutations identified, 26 (60.5%) were predicted by at least two tools to have an impact on protein function. To our knowledge, this is the first study to use in silico approaches to determine the impact of OBI-associated mutations, thereby identifying potential candidates for functional analysis to facilitate mechanistic studies of the OBI phenotype.

GENE INTERACTIONS OF ALPHA-ADDUCIN AND LANOSTEROL SYNTHASE IMPACT RENAL IMPAIRMENT IN SALT SENSITIVE HYPERTENSION

Objective: The genes involved in the development of renal damage and salt sensitive hypertension (SS) are unknown. Renal impairment is considered to be the major determinant of salt sensitive hypertension. Design and method: We explored the roles of alpha-adducin (ADD1) and lanosterol synthase (LSS), genes coding for structural proteins of the cell membrane and Endogenous Ouabain (EO), respectively, on renal Na handling and their genetic interactions in a large cohort of naïve hypertensive patients (NHP) whose salt sensitive phenotype was characterized. Acute saline load (NaCl 308 mEq/2 h e.v.) was performed in 774 NHP (age 44.95 ± 9.61 years), and functional and hormone renal parameters were tested. Results: Under baseline conditions NHP carriers of the LSS AA genotype showed lower GFR (n = 68, 115.7 ± 4.6 ml/min) compared to LSS C carriers (124.6 ± 1.4 ml/min, p = 0.066). After an acute saline test, GFR increased in both groups, while the urinary volume and urinary creatinine were lower in LSS AA. Analysis of gene*gene interactions demonstrated that NHPs carrying both mutated GT ADD1 and homozygous for LSS C variants excreted the sodium load more rapidly than their ADD1*LSS mutated variants. On the other hand, an additive (p = 0.003) effect of ADD1 GT & LSS AA variants on the pressure-natriuresis relationship was observed, with a significant right shift along the x axis. Finally, circulating EO was modified according to the LSS variant: in SS LSS AA, EO rose signicantly during the recovery while in SR LSS AA, EO was suppressed as were aldosterone and PRA. Conclusions: The results demonstrate: 1. NHPs carrying the LSS AA genotype have reduced GFR under basal conditions; 2. Salt Sensitive LSS AA are EO non-modulators, since their circulating EO does not decline under circumstances where the RAAS is suppressed; 3. The ADD1*LSS interaction identifies those NHPs with impaired renal Na handling.

Analysis of hepatitis B virus (HBV) preS1, preS2 and S gene regions from patient groups infected with HBV genotype D

Mutations in preS and S gene regions of hepatitis B virus genome may cause immune escape and diagnostic escape HBV mutants. The aim of this study was to determine preS1, preS2 and S gene regions of HBV from HBV infected patient groups by sequence analysis and contribute to the relevant literature. Nucleic acid sequence analysis of preS and S genes of HBV PCR products from 56 archived plasma samples sent to Ege University Faculty of Medicine Medical Microbiology Department Molecular Virology laboratory, for HBV tests were determined by chain termination reaction. Amino acid (aa) sequences were compared with the reference sequences obtained from GenBank. Plasma samples belonged to four groups of patients: A- Chronic HBV infected patients with typical HBV serological profiles (22 samples), B- HBV infected patients with atypical HBV serological profiles (26 samples), C- HBV re-infected patients after liver transplantation (5 samples), D- Seroconversion phase following acute HBV infection (3 samples). One of two vaccine escape mutant samples was also diagnostic escape mutant; the other diagnostic escape mutant was isolated from anti-HBc positive sample. All of the sequences were determined as genotype D. HBsAg subtypes were determined as; two ayw1, six ayw3, two mix, 46 ayw2. Among the 304 codons analysed between preS 33rd and S 162nd amino acids; aa variants were determinedin 105 codons (34.5%). Sequences can be found in GenBank with accession numbers FJ001941-FJ001996. At least one aa variation was detected in 48 of 56 samples (85.7%). The amino acid variants were as follows; PreS1: A33T, A39T, P41K, D44del, D50N, T51P, D54N, L65P/M, F67L, W77T, A81S, Q82E, I84T, L85I/M, Q86H/T, L88S, A90T/V, N91K/del, A95P, S96A, T97I/A, N98K, Q100K, S101T, S109T, P110S, N114D/E, PreS2: M1V, Q2R, S5H, F8S, H9Q, Q13L, D14N, R16K, R18K, G19S/D, F22L/S, S28T, G30E, N33T, V39A, P41H/L, I42T/L, I45T, F46Y, S47L, R48K, I49T, D51V/G, P52L, A53V, L54R/G, N55K; S gene: E2D, I4F, F8L, G10A, V14A, F20S, L22del, R24K, P29L, Q30K, N40S, F41del, G44E, T45L, T46P, V47A, L49R, Q54R, P56L, S64F, P70A, M75I, C76Y, R79H, I81T, F83C, L88P, L94S, Y100F, Q101H/R, M103L, L104F, L109I/M, I110L, G112S/R, S113N/P, S114A/del, T115I, T116N, T118A/K, P120A/T, T123A, in "a" determinant; T126I, Q129H/R, T131N, M133T, Y134N, S136Y, S143L/M/T, D144E, G145A/R. Deletions were also found in all three preS/S gene regions. The highest number of aa variations were detectedin the isolated anti-HBc positive sample (in 24 codons), followed by liver transplant group (8-13 codons). Point mutation was detected in the preS2/S promoter CCAAT box. Major hydrophilic region (MHR) variants were determined in 41.1% of 56 samples. The highest number of MHR variants belonged to atypical HBV serological profile group (group B; 61.5%) and liver transplantation group with HBV re-infection (all C group). Among the diagnostic escape and immune escape mutant (anti-HBs positive) samples, reported MHR and "a" determinant mutations were detected. In conclusion, the study population carries HBV preS/S variants; MHR and "a" determinant variant rates are high among diagnostic or immune escape mutants. It is important to evaluate the mutant detection performance of HBsAg tests.

Gene–Gene Interactions Between Glutathione S-Transferase M1 and Matrix Metalloproteinases 1, 9, and 12 in Chronic Obstructive Pulmonary Disease in Serbians

ABSTRACTChronic obstructive pulmonary disease (COPD) is a complex disorder influenced by multiple genetic and environmental factors, as well as their interactions. Since elevated oxidative stress and protease activity characterize the pathogenesis of COPD, variants of genes that can affect these processes have been commonly studied in COPD. However, interactions among genes that can influence oxidative stress and protease activity remain poorly investigated in COPD. The aim of this study was to look into the role of functional variants in matrix metalloproteinases (MMPs) 1, 9, and 12 in the occurrence and/or modulation of COPD, and to analyze their interactions with glutathione S-transferases (GSTs) M1, T1, and P1 in the pathogenesis of COPD in Serbians. The MMP1 rs1799750 G > GG, MMP9 rs3918242 C > T, and MMP12 rs2276109 A > G variants were analyzed by direct detection methods. Gene–gene interactions between variants in MMPs and GSTs were assessed using a case-control model. Our results showed association of the MMP1 GG/GG genotype with COPD (p = 0.036, OR = 2.50). Gene–gene interactions between the GSTM1 null and MMP1 GG (p = 0.028, OR = 2.99) and the GSTM1 null and MMP12 AA variants (p = 0.015, OR = 3.82) were found to significantly increase the risk of COPD occurrence. Furthermore, the MMP12 G variant was found to modify the age of COPD onset (p = 0.025, OR = 3.30), while interaction between the GSTM1 null and MMP9 T variants was found to modify the severity of disease (p = 0.019, OR = 4.83). To our best knowledge, this is the first study revealing several gene–gene interactions affecting oxidative stress and protease activity in the pathogenesis of COPD.

TLR2 2258 G>A single nucleotide polymorphism and the risk of congenital infection with human cytomegalovirus

BackgroundHuman cytomegalovirus (HCMV) is responsible for the most common intrauterine infections, which may be acquired congenitally from infected pregnant woman to fetus. The research was aimed to estimate the role of three single nucleotide polymorphisms (SNPs) located in TLR2 gene, and the common contribution of TLR2, and previously studied TLR4 and TLR9 SNPs, to the occurrence of congenital HCMV infection in fetuses and newborns.MethodsThe study was performed in 20 Polish fetuses and newborns, congenitally infected with HCMV, and in 31 uninfected controls, as well as with participation of pregnant women, the mothers of 16 infected and 14 uninfected offsprings. Genotypes in TLR2 SNPs were determined, using self-designed nested PCR-RFLP assays, and confirmed by sequencing. The genotypes were tested for Hardy-Weinberg (H-W) equilibrium, and for their relationship with the development of congenital cytomegaly, using a logistic regression model. The common influence of TLR2, TLR4 and TLR9 SNPs on the occurrence of congenital disease was estimated by multiple-SNP analysis.ResultsDistribution of the genotypes and alleles in TLR2 1350 T>C and 2029 C>T SNPs was similar between the studied groups of fetuses and neonates. In case of 2258 G>A polymorphism, the GA heterozygotic status was significantly more frequent in the infected cases than among the uninfected individuals (25.0% vs. 3.2%, respectively), and increased the risk of HCMV infection (OR 10.00, 95% CI 1.07–93.44; P ≤ 0.050). Similarly, the A allele within 2258 G>A polymorphism was significantly more frequent among the infected offsprings than in the uninfected ones (12.5% vs. 1.6%; P ≤ 0.050). Complex AA variants for both TLR2 2258 and TLR9 2848 G>A polymorphisms, were estimated to be at increased risk of congenital HCMV infection (OR 11.58, 95% CI 1.19–112.59; P ≤ 0.050). Additionally, significant relationships were observed between the occurrence of complex AA or GA variants for both TLR2 and TLR9 SNPs and the increased viral loads, determined in fetal amniotic fluids and in maternal blood or urine specimens (P ≤ 0.050).ConclusionsAmong various TLR2, TLR4 and TLR9 polymorphisms, TLR2 2258 G>A SNP seems to be an important factor associated with increased risk of congenital HCMV infection in Polish fetuses and neonates.