TaqMan Single Nucleotide Polymorphisms Research Articles

TLR9 rs352139 Genetic Variant Promotes Tacrolimus Elimination in Chinese Liver Transplant Patients During the Early Posttransplantation Period.

There are limited markers that could facilitate individualized tacrolimus treatment in the early posttransplantation period. Genetic factors have been found to play critical roles in determining tacrolimus pharmacokinetics. We aimed to examine the association of donor and recipient Toll-like receptor (TLR) polymorphisms with tacrolimus elimination and the potential mechanism for TLR gene polymorphism-mediated tacrolimus metabolism. Two independent cohorts including 297 patients receiving liver transplantation (LT) were enrolled in this study (cohort A was composed of 200 patients; cohort B included 97 patients and served as a validation set). Toll-like receptors polymorphisms were genotyped using TaqMan single nucleotide polymorphisms (SNPs) assays. The protein expressions were detected by Western blotting. The metabolism assay was used to quantify tacrolimus elimination. The activity of nuclear factor-kB (NF-kB) was evaluated by luciferase reporter assay. Tacrolimus dose-adjusted trough blood concentrations (C/D) ratios were significantly lower for donor TLR9 rs352139 AG/GG carriers than AA carriers at weeks 1, 2, and 3 after LT. In multivariate analysis, donor and recipient CYP3A5 rs776746 and donor TLR9 rs352139 were independent predictors of tacrolimus C/D ratios in the early period after transplantation in both cohorts. When investigating the combined effects of donor CYP3A5 rs776746 and donor TLR9 rs352139 genotypes, the C/D ratios were remarkably significant at all time points during the first month after LT within the four groups. Furthermore, CYP3A5 mRNA expression in liver tissue was significantly higher for AG/GG patients than AA carriers after LT. In addition, we demonstrated that the TLR9 rs352139 genetic variant promotes tacrolimus metabolism of liver cells via upregulation of CYP3A5, which is dependent on the repression of NF-κB/pregnane X receptor (PXR) signaling. Donor TLR9 rs352139 genetic variant facilitated tacrolimus elimination during the early stage after LT in Chinese patients, which might be related to the upregulation of CYP3A5 enzyme via the NF-kB/PXR signaling pathway.

CYP2C9 polymorphism is not associated with elevated carcinoembryonic antigen levels

Background: Carcinoembryonic antigen (CEA) is a glycoprotein that can be elevated in a number of benign and malignant conditions. In colorectal cancer, it is used as a prognostic marker and to detect recurrence. However, it lacks specificity and may become elevated in individuals without a history of cancer or other identifiable cause leading to costly and invasive investigation. Objective: The aim of this study was to assess whether genetic polymorphisms in the liver enzyme CYP2C9 could explain high CEA levels in otherwise normal individuals. Design: This is a case-control study. Setting: Individuals were genotyped for the poor metabolizer (PM) alleles CYP2C9*2 and CYP2C9*3 using predesigned TaqMan single nucleotide polymorphisms assays. Patients and Methods: Nineteen individuals with previously clinically unexplained elevated CEA and 567 healthy Caucasian controls were included. Main Outcome Measures: Chi-square analysis was used to test for association of CYP2C9 genotype with plasma CEA concentration. Sample Size: Nineteen individuals with previously clinically unexplained elevated CEA and 567 healthy Caucasian controls were included. Results: Fifteen of the 19 individuals with previously high CEA had elevated plasma CEA (>3.0μg/L) on re-testing. The frequency of CYP2C9 PM alleles in these 15 patients was not significantly higher than the frequency in controls. Conclusion: CEA concentrations do not appear to be influenced by CYP2C9 genotype, so this cannot be used to explain elevated CEA in the absence of an obvious clinical cause. Limitation: Small sample size.

12-Week aerobic exercise and nutritional program minimized the presence of the 64Arg allele on insulin resistance.

The objective of the study was to investigate the response of 64Arg allele carriers of the ADRB3 gene (Trp64Arg polymorphism) in the anthropometric, cardiorespiratory and metabolic variables in overweight adolescents after a 12-week aerobic exercise and nutritional program. A total of 92 overweight adolescents, 10-16 years old and of both genders, participated. Body composition, waist circumference (WC), pubertal stage status, blood pressure, glucose, insulin and lipid profile and direct maximal oxygen uptake were assessed at baseline and after 12 weeks of a training program. The homeostasis metabolic assessments [homeostasis model assessment of insulin resistance (HOMA-IR)] and quantitative insulin sensitivity check index (QUICKI) were determined and the Trp64Arg polymorphism of the ADRB3 gene was investigated by Taqman single nucleotide polymorphism (SNP) genotyping assays. Exercise sessions consisted of 100-min aerobic exercise and 20-min stretching, 3 times a week, totalizing 36 sessions. Multivariate analysis of variance (MANOVA), analysis of covariance (ANCOVA) and effect size were used for variables, with p<0.05 considered significant. In baseline, HOMA-IR was higher in carriers of the 64Arg allele and decreased more after 12 weeks than in non-carriers (p=0.01). The anthropometric, physical fitness and metabolic profiles had similar responses after training in carriers and non-carriers. Overweight adolescents present changes in body composition and physical fitness, independent of Trp64Arg genotypes. However, a 12-week aerobic exercise and nutritional program promoted greater reductions in insulin resistance in carriers of the 64Arg allele.

SH2B3 (lnk) Regulates Type 1 Diabetes Immune Phenotypes

Background: The type 1 diabetes (T1D)-associated risk gene SH2B Adaptor Protein 3 (SH2B3) encodes a phosphatase with specificity for Janus Kinase 2 (JAK2). We hypothesized that variations in SH2B3 would affect immune signaling pathways relevant to T1D autoimmunity. Here we report: 1) Occurrence of the SH2B3 risk variant among T1D patients, unaffected first-degree relatives and controls; 2) Prevalence of SH2B3 risk genotype in African Americans in the Southeastern U.S.; and 3) Alterations to immune composition associated with the SH2B3 risk variant. Approach and Results: 1) The University of Florida Diabetes Institute (UFDI) cohort (n=1946) was analyzed for genetic risk of T1D using a Taqman single nucleotide polymorphism (SNP) genotyping array with coverage of 32 SNPs. Two SNPs (rs3184504 and rs653178) corresponding to SH2B3 were in perfect linkage disequilibrium and will be described here as minor (T1D risk) or common variant. Among Caucasian subjects, the odds ratio (OR) for the minor variant among T1D subjects was 1.30 (1.06-1.59, p=1.42x10-2), similar to previous reports. Among African American subjects, the minor variant OR was elevated (2.93, 1.22-7.03, p=1.30x10-2), representing the most highly-associated non-HLA gene. Complete blood count (CBC, n=954) and flow cytometric human immunophenotyping (HIP, n=252) were performed on a subset of subjects. Individuals carrying the risk variant of SH2B3 had significantly more blood monocytes and neutrophils but similar numbers of lymphocytes compared to non-carriers. HIP revealed a significantly higher frequency of type 1 (CXCR3+) CD8+ T cells in subjects with the risk variant of SH2B3. Conclusions: The risk variant of SH2B3 is associated with both increased risk for T1D and seroconversion in Caucasian and African American subjects. Phenotypically, this element of T1D genetic risk presents as increased frequency of some myeloid cell populations and either expansion or polarization of CD8+ T cells bearing the canonical Th1 chemokine receptor CXCR3. Disclosure A. Camargo: None. D.J. Perry: None. T.M. Brusko: Stock/Shareholder; Self; OneVax, LLC. Advisory Panel; Self; Caladrius Biosciences, Inc.. Consultant; Self; Merck &amp; Co., Inc., Sanofi-Aventis. M.A. Wallet: None.

F194. ASSOCIATION STUDY BETWEEN TREATMENT RESPONSE OF AMISULPRIDE AND DOPAMINE D3 RECEPTOR GENE POLYMORPHISMS

BackgroundThe aim of this study is to evaluate the association between rs6280 and rs905568 genetic polymorphism of DRD3 gene and the treatment response of amisulpride.MethodsAfter six weeks treatment of amisulpride, 125 schizophrenia patients were interviewed based on the Positive and Negative Syndrome Scale (PANSS) and the Clinical Global Impression-Severity (CGI-S). The genotyping for rs6280 and rs905568 was performed using TaqMan single nucleotide polymorphism (SNP) genotyping assay.ResultsThere was no significant difference in the frequency of genotype and allele of rs6280 between the responders and non-responders based on the total, positive, and general score of PANSS and CGI-S score. However, there was a significant association between this SNP and treatment response in the negative score of PANSS (χ2 = 5.23, p = 0.022). There was no significant association between rs905568 and the response in positive, negative, general, and total PANSS score and CGI-S score.DiscussionThis is the first positive association study between DRD3 gene and the treatment response of negative symptoms to amisulpride in Korean schizophrenia patients. A larger scale research on more SNP of the DRD3 gene will make a progress in the study of pharmacogenetics on the treatment response of the amisulpride.

Role of selected polymorphisms in determining muscle fiber composition in Japanese men and women.

Genetic polymorphisms and sex differences are suggested to affect muscle fiber composition; however, no study has investigated the effects of genetic polymorphisms on muscle fiber composition with respect to sex differences. Therefore, the present study examined the effects of genetic polymorphisms on muscle fiber composition with respect to sex differences in the Japanese population. The present study included 211 healthy Japanese individuals (102 men and 109 women). Muscle biopsies were obtained from the vastus lateralis to determine the proportion of myosin heavy chain (MHC) isoforms (MHC-I, MHC-IIa, and MHC-IIx). Moreover, we analyzed polymorphisms in α-actinin-3 gene (ACTN3; rs1815739), angiotensin-converting enzyme gene (ACE; rs4341), hypoxia-inducible factor 1 α gene (rs11549465), vascular endothelial growth factor receptor 2 gene (rs1870377), and angiotensin II receptor, type 2 gene (rs11091046), by TaqMan single-nucleotide polymorphism genotyping assays. The proportion of MHC-I was 9.8% lower in men than in women, whereas the proportion of MHC-IIa and MHC-IIx was higher in men than in women (5.0 and 4.6%, respectively). Men with the ACTN3 RR + RX genotype had a 4.8% higher proportion of MHC-IIx than those with the ACTN3 XX genotype. Moreover, men with the ACE ID + DD genotype had a 4.7% higher proportion of MHC-I than those with the ACE II genotype. Furthermore, a combined genotype of ACTN3 R577X and ACE insertion/deletion (I/D) was significantly correlated with the proportion of MHC-I (r = −0.23) and MHC-IIx (r = 0.27) in men. In contrast, no significant correlation was observed between the examined polymorphisms and muscle fiber composition in women. These results suggest that the ACTN3 R577X and ACE I/D polymorphisms independently affect the proportion of human skeletal muscle fibers MHC-I and MHC-IIx in men but not in women.NEW & NOTEWORTHY In men, the RR + RX genotype of the α-actinin-3 gene (ACTN3) R577X polymorphism was associated with a higher proportion of myosin heavy chain (MHC)-IIx. The ID + DD genotype of the angiotensin-converting enzyme gene (ACE) insertion/deletion (I/D) polymorphism, in contrast to a previous finding, was associated with a higher proportion of MHC-I in men. In addition, the combined genotype of these polymorphisms was correlated with the proportion of MHC-I and MHC-IIx in men. Thus ACTN3 R577X and ACE I/D polymorphisms influence the muscle fiber composition in Japanese men.

Association between inducible nitric oxide synthase gene polymorphism and ischemic cardio-cerebrovascular disease in Chinese Han population

Objective To evaluate the association between inducible nitric oxide synthase (iNOS) gene polymorphisms and ischemic cardio-cerebrovascular disease in Chinese Han population. Methods Two independent case-control studies were conformed, including 291 cases of coronary heart disease (CHD) and 487 healthy subjects, 246 cases of ischemic stroke and 246 healthy subjects. The genotype of rs2779248(C/T) and rs1137933(C/T) were determined by Taqman single nucleotide polymorphism (SNP) genotyping assays. Results T allele of rs2779248 and rs1137933 may increase the risk for CHD or ischemic stroke in Chinese Han population. combined with the two independent case-control studies, the risk relationship also existed. T allele had higher risk for ischemic cardio-cerebrovascular disease than C allele with the odds ratio being 1.33 [95% confidence interval (CI): 1.09-1.61] for rs2779234, and 1.42 (95%CI: 1.16-1.73) for rs1137933, respectively. Adjusted by conventional risk factors, rs2779248 TT genotype still was a risk factor for ischemic cardio-cerebrovascular disease [odds ratio (OR)=2.75, 95%CI: 1.38-5.49]. As compared with CC genotype, individual with CT+ TT genotype of rs1137933 had higher risk with the odds ratio being 1.37 (95%CI: 1.03-1.82). Conclusion Our study revealed the polymorphisms of rs2779248 and rs1137933 in iNOS gene were associated with ischemic cardio-cerebrovascular disease in Chinese Han population. Key words: Inducible nitric oxide synthase gene; Ischemic cardio-cerebrovascular disease; Genetic polymorphism; Risk factors

A polymorphism in the glucocorticoid receptor gene is associated with refractory hypotension in premature infants

Glucocorticoids play an important role in endocrine control. The association of glucocorticoid receptor (GR) gene polymorphisms with altered sensitivity to glucocorticoid therapy has been reported in adults. However, there are few such reports in infants. The present study analyzed the prevalence of four GR polymorphisms in preterm infants born before 30 weeks of gestation and determined the associations between these polymorphisms and clinical outcomes in the infants. Totally, 41 preterm infants born at two hospitals in Fukushima were retrospectively screened for the presence of four GR gene polymorphisms, using a TaqMan single-nucleotide polymorphism genotyping assay. The effect of GR gene polymorphisms on clinical outcomes during hospitalization was evaluated. The following primary clinical outcomes were assessed: refractory hypotension in the acute phase and/or severe bronchopulmonary dysplasia, maximum dopamine and dobutamine doses administered, and total hydrocortisone dose administered in the first 48h of life. Multivariate analysis with logistic regression was used to assess the association between clinical factors and refractory hypotension. Of the four GR polymorphisms, only the BclI polymorphism was detected. The genotype distribution was as follows: C/C, 33; C/G, 8; and G/G, 0 infants. Significant differences were observed between the C/C and C/G genotypes with respect to the following variables: refractory hypotension (6% vs. 50%), dopamine dose [3.0 (2.0-4.0) vs. 4.8 (4.0-7.5) μg/kg/min], dobutamine dose [2.4 (0.0-3.6) vs. 4.0 (0-10.0) μg/kg/min], and total hydrocortisone dose administered in the first 48h of life [2.0 (0-10.0) vs. 6.0 (0-12.0) mg/kg]. Multivariate analysis showed that the BclI genotype (C/C) was significantly less associated with refractory hypotension in the acute phase (odds ratio, 0.008; 95% confidence interval, 0.000-0.371; p=0.013). The incidence of refractory hypotension in infants with the C/C genotype was initially expected to be higher than that in infants with the C/G genotype. However, the results of this study were rather different from what we originally expected. The suppressive effect of antenatal steroid use on the HPA axis of the preterm infants with the BclI variant may be associated with refractory hypotension in the acute phase.

Anti–Tumor Necrosis Factor With a Glyco-Engineered Fc-Region Has Increased Efficacy in Mice With Colitis

Although tumor necrosis factor (TNF) antagonists reduce many clinical features of inflammatory bowel disease, complete mucosal healing occurs in fewer than 50% of patients. The Fc-region of monoclonal antibodies against TNF has immunosuppressive properties via effects on macrophage polarization. We examined the interaction between the anti-TNF Fc-region and Fcγ receptors (FcγR), and whether the absence of the Fc core fucose (which increases binding to FcγRIIIa) increases the efficacy of anti-TNF in mice with colitis. We generated Rag1-/- mice that lackall activating FcγRs (FcγRI, FcγRIII, and FcγRIV; called FcγR-/-Rag1-/- mice). We produced hypo-fucosylated antibodies against mouse and human TNF (adalimumab). Colitis was induced in mice by transfer of CD4+CD45RBhi to FcγR-/-Rag1-/- or Rag1-/- littermates; mice were given different antibodies against TNF or isotype (control) antibodies and disease activity index scores were determined. Colon tissues were collected and analyzed by histology. Human peripheral blood mononuclear cells (PBMCs) were isolated from blood of healthy donors. T-cell proliferation and proportions of CD206+ (immune regulatory) macrophages were measured in mixed lymphocyte reactions. Human PBMCs were genotyped for FCGR3A158 (the FcγRIIIa-158F allotype displays a lower Fc binding affinity) using the TaqMan single nucleotide polymorphism genotype assay. Rag1-/- mice with colitis given anti-TNF had near complete mucosal healing and Rag1-/- mice given an isotype control antibody developed severe colitis. In contrast, FcγR-/-Rag1-/- mice were refractory to the effects of anti-TNF: their histological colitis scores were as severe as those from FcγR-/-Rag1-/- mice given a control antibody. Colons from Rag1-/- mice that received anti-TNF had an increased number of CD206+ macrophages compared with Rag1-/- mice given control antibody; in FcγR-/-Rag1-/- mice given anti-TNF these numbers were as low as FcγR-/-Rag1-/- given the control antibody. In human PBMCs, anti-TNF increased the number of CD206+ macrophages: this required expression of FcγRIIIa; numbers of these cells were reduced in PBMCs with the low-affinity FcγRIIIa-158F genotype. A hypo-fucosylated form of adalimumab bound human FcγRIIIa with a higher affinity than control adalimumab. When hypo-fucosylated adalimumab was added to PBMCs, a larger number of CD206+ macrophages formed and T-cell proliferation was reduced, compared with addition of a control adalimumab. Hypo-fucosylated adalimumab increased the number of CD206+ macrophages in PMBCs that expressed the low-affinity FcγRIIIa. In mice with colitis, hypo-fucosylated anti-TNF significantly increased the number of CD206+ macrophages in the colon compared with control anti-TNF and was more effective in reducing colitis severity as measured by histology. In a study of the invitro and invivo mechanisms of anti-TNF, we found FcγR engagement by anti-TNF to be required for reduction of colitis in mice and development of CD206+ macrophages. A hypo-fucosylated form of anti-TNF binds FcγRIIIa with higher affinity and induces development of CD206+ macrophages in human PBMCs, especially PBMCs that express low-affinity FcγRIIIa. Hypo-fucosylated anti-TNF might be more effective in patients with inflammatory bowel disease.

The association among cytochrome P450 3A, progesterone receptor polymorphisms, plasma 17-alpha hydroxyprogesterone caproate concentrations, and spontaneous preterm birth

Infants born <37 weeks' gestation are of public health concern since complications associated with preterm birth are the leading cause of mortality in children <5 years of age and a major cause of morbidity and lifelong disability. The administration of 17-alpha hydroxyprogesterone caproate reduces preterm birth by 33% in women with history of spontaneous preterm birth. We demonstrated previously that plasma concentrations of 17-alpha hydroxyprogesterone caproate vary widely among pregnant women and that women with 17-alpha hydroxyprogesterone caproate plasma concentrations in the lowest quartile had spontaneous preterm birth rates of 40% vs rates of 25% in those women with higher concentrations. Thus, plasma concentrations are an important factor in determining drug efficacy but the reason 17-alpha hydroxyprogesterone caproate plasma concentrations vary so much is unclear. Predominantly, 17-alpha hydroxyprogesterone caproate is metabolized by CYP3A4 and CYP3A5 enzymes. We sought to: (1) determine the relation between 17-alpha hydroxyprogesterone caproate plasma concentrations and single nucleotide polymorphisms in CYP3A4 and CYP3A5; (2) test the association between progesterone receptor single nucleotide polymorphisms and spontaneous preterm birth; and (3) test whether the association between plasma concentrations of 17-alpha hydroxyprogesterone caproate and spontaneous preterm birth varied by progesterone receptor single nucleotide polymorphisms. In this secondary analysis, we evaluated genetic polymorphism in 268 pregnant women treated with 17-alpha hydroxyprogesterone caproate, who participated in a placebo-controlled trial to evaluate the benefit of omega-3 supplementation in women with history of spontaneous preterm birth. Trough plasma concentrations of 17-alpha hydroxyprogesterone caproate were measured between 25-28 weeks of gestation after a minimum of 5 injections of 17-alpha hydroxyprogesterone caproate. We extracted DNA from maternal blood samples and genotyped the samples using TaqMan (Applied Biosystems, Foster City, CA) single nucleotide polymorphism genotyping assays for the following single nucleotide polymorphisms: CYP3A4*1B, CYP3A4*1G, CYP3A4*22, and CYP3A5*3; and rs578029, rs471767, rs666553, rs503362, and rs500760 for progesteronereceptor. We adjusted for prepregnancy bodymass index, race, and treatment group in a multivariable analysis. Differences in the plasma concentrations of 17-alpha hydroxyprogesterone caproate by genotype were evaluated for each CYP single nucleotide polymorphism using general linear models. The association between progesterone receptor single nucleotide polymorphisms and frequency of spontaneous preterm birth was tested using logistic regression. A logistic model also tested interaction between 17-alpha hydroxyprogesterone caproate concentrations with each progesterone receptor single nucleotide polymorphism for the outcome of spontaneous preterm birth. The association between CYP single nucleotide polymorphisms *22, *1G, *1B, and *3 and trough plasma concentrations of 17-alpha hydroxyprogesterone caproate was not statistically significant (P= .68, .44, .08, and .44, respectively). In an adjusted logistic regression model, progesterone receptor single nucleotide polymorphisms rs578029, rs471767, rs666553, rs503362, and rs500760 were not associated with the frequency of spontaneous preterm birth (P= .29, .10, .76, .09, and .43, respectively). Low trough plasma concentrations of 17-alpha hydroxyprogesterone caproate were statistically associated with a higher frequency of spontaneous preterm birth (odds ratio, 0.78; 95% confidence ratio, 0.61-0.99; P= .04 for trend across quartiles), however no significant interaction with the progesterone receptor single nucleotide polymorphisms rs578029, rs471767, rs666553, rs503362, and rs500760 was observed (P= .13, .08, .10, .08, and .13, respectively). The frequency of recurrent spontaneous preterm birth appears to be associated with trough 17-alpha hydroxyprogesterone caproate plasma concentrations. However, the wide variation in trough 17-alpha hydroxyprogesterone caproate plasma concentrations is not attributable to polymorphisms in CYP3A4 and CYP3A5 genes. Progesterone receptor polymorphisms do not predict efficacy of 17-alpha hydroxyprogesterone caproate. The limitations of this secondary analysis include that we had a relative small sample size (n= 268) and race was self-reported by the patients.

Apolipoprotein C-I Polymorphism and Its Association with Serum Lipid Levels and Longevity in the Bama Population.

This study aims to determine the association between the apolipoprotein C-I polymorphism and the longevity and genetic variants in ApoC-I that can influence the serum lipid levels in Bama. ApoC-I genotypes were determined by Taqman single nucleotide polymorphism (SNP) genotyping assays in 178 long-lived inhabitants (longevity group aged from 90 to 110 years), 147 healthy controls (Control 1 group aged from 40 to 79 years old) from Bama County, and 190 healthy controls (Control 2 group aged from 40 to 79 years old) from Nandan County without a family history of longevity. Statistical analysis was conducted using SPSS 16.0. All genotype distributions of rs584007 and rs4420638 were consistent with the Hardy–Weinberg equilibrium (p > 0.05). Significant differences were observed in the frequencies of the three genotypes (GG, AG, and AA) among the longevity and the two control groups (χ2 = 11.238, p = 0.024) for rs584007. No significant differences were observed in the frequencies of the three genotypes (GG, AG, and AA) among the longevity and the two control groups (χ2 = 4.587, p = 0.318) for rs4420638. The levels of total cholesterol (TC), triglycerides (TG), high-density lipoprotein-cholesterol (HDL-c), and low-density lipoprotein-cholesterol (LDL-c) were not different among the three genotypes of rs584007 in the three groups. The levels of HDL-c for GG, AG, and AA were significantly different (the highest being in the longevity group), while the levels of TG for AA and AG genotypes (the lowest being in the longevity group) and the levels of LDL-c for AG were significantly different (p < 0.05) among the three groups for rs584007. The levels of TG and HDL-c were significantly different among the three rs4420638 genotypes in the longevity group. The levels of TC for GG, AG, and AA were significantly different in the Control 2 group, while the levels of TG and HDL-c for AA and AG genotypes were significantly different (p < 0.05) among the three groups for rs4420638. The level of HDL-c was highest in the longevity group for AA and AG genotypes, and the level of TG was highest in the Control 2 group for rs4420638. Serum lipid parameters were related to environmental factors, including age, gender, BMI, DBP, SBP, rs4420638, and rs584007. The ApoC-I polymorphism might be one of the genetic factors of longevity in Bama. The ApoC-I rs4420638 and rs584007 SNPs are associated with serum TG and HDL-c levels in the longevous population.

Associations of VEGF Gene Polymorphisms With Erectile Dysfunction and Related Risk Factors

BackgroundRepeated evidence from animal models suggests a strong link between vascular endothelial growth factor (VGEF) and penile vasculature and erectile function because VEGF can alter the physiologic pathways involved in the regulation of penile vasomotor tone. AimTo investigate three VEGF polymorphisms and their link to erectile dysfunction (ED). MethodsWe enrolled 688 Taiwanese men with a mean age of 55.6 years (SD = 4.5) during a free health screening. All participants provided complete medical histories and underwent physical examinations. Fasting blood samples were obtained for biochemical analysis and hormone profiling. The allelic discrimination of three VEGF gene polymorphisms (460T/C [rs833061], 1154G/A [rs1570360], and 2578A/C [rs699947]) was performed using validated TaqMan single-nucleotide polymorphism genotyping assays. OutcomesSubjects underwent assessment using the simplified five-item International Index of Erectile Function to diagnose and assess ED severity. ResultsThe results showed that diabetes mellitus (odds ratio [OR] = 3.27, P < .01), hypertension (OR = 3.47, P < .01), and having the VEGF 2578A allele (OR = 1.54, P = .01) were the three most independent risk factors for ED. In univariate analysis, all three VEGF polymorphisms (460C, 1154A, and 2578A) were significantly associated with a higher prevalence of coronary artery disease (P < .01) and greater frequencies of hypertension were found in carriers of the 1154A allele and the 2578A allele (P = .01). Multiple logistic regression analysis showed a significant association between VEGF 2578A allele carrier status and ED (OR = 1.54, 95% CI = 1.10∼2.15, P = .01). Furthermore, the prevalence and severity of ED were significantly increased with an increment of the 2578A allele number (P < .05). Clinical ImplicationsVEGF 2578C/A gene polymorphisms could be a genetic susceptibility factor for the development of ED. Strength and LimitationThis is the first study to investigate the genetic susceptibility of VEGF polymorphisms to ED. This study was cross-sectional with a lack of functional and molecular production investigations. Data on the association among conditions might not allow definitive conclusions about causal links. ConclusionThis study showed that VEGF 2578A allele carriers in a Taiwanese population are at greater risk for ED.Lee Y-C, Huang S-P, Tsai C-C, et al. Associations of VEGF Gene Polymorphisms With Erectile Dysfunction and Related Risk Factors. J Sex Med 2017;14:510–517.

Development and application of a TaqMan single nucleotide polymorphism genotyping assay to study infectious laryngotracheitis virus recombination in the natural host.

To date, recombination between different strains of the avian alphaherpesvirus infectious laryngotracheitis virus (ILTV) has only been detected in field samples using full genome sequencing and sequence analysis. These previous studies have revealed that natural recombination is widespread in ILTV and have demonstrated that recombination between two attenuated ILTV vaccine strains generated highly virulent viruses that produced widespread disease within poultry flocks in Australia. In order to better understand ILTV recombination, this study developed a TaqMan single nucleotide polymorphism (SNP) genotyping assay to detect recombination between two field strains of ILTV (CSW-1 and V1-99 ILTV) under experimental conditions. Following in vivo co-inoculation of these two ILTV strains in specific pathogen free (SPF) chickens, recovered viruses were plaque purified and subjected to the SNP genotyping assay. This assay revealed ILTV recombinants in all co-inoculated chickens. In total 64/87 (74%) of the recovered viruses were recombinants and 23 different recombination patterns were detected, with some of them occurring more frequently than others. The results from this study demonstrate that the TaqMan SNP genotyping assay is a useful tool to study recombination in ILTV and also show that recombination occurs frequently during experimental co-infection with ILTV in SPF chickens. This tool, when used to assess ILTV recombination in the natural host, has the potential to greatly contribute to our understanding of alphaherpesvirus recombination.

Associations Between Apolipoprotein-A5 Genotype, High-Fat Diet and Plasma Lipid Levels among HIV-infected Children Initiating Antiretroviral Therapy in India

Background Both antiretroviral therapy (ART) and polymorphism in genes involved in lipoprotein metabolism contribute to the development of ART-induced dyslipidemia. Apolipoprotein A5 (APOA5)gene variant, which vary by race/ethnicity, influence plasma lipid concentrations. We explored the association of candidate gene effect on plasma lipid levels with food in HIV-infected children initiating ART in south India.Methods HIV-infected children, between 2 and 12 years of age initiating non-nucleoside reverse transcriptase inhibitor (NNRTI)-based ART during 2010–2014 were included. They were assessed for their dietary intake by 24-hour dietary recall. Fasting blood was drawn for serum triglycerides (TGL), total cholesterol and high-density cholesterol along with CD4 cell count, and HIV-1 viral load. APOA5 gene polymorphisms rs662799, rs3135506 were determined by Taqman single-nucleotide polymorphism (SNP) genotyping assays. The General Linear Model (GLM) was applied to explore the risk of hypertriglyceridemia for SNP’s rs662799 and rs3135506 with food interaction in children.ResultsThree hundred and ninety HIV-infected children {median age (IQR): 9 (5–11) years; and median viral load: 141,000 (25,876–436,000) copies/mL} were started on NNRTI-based ART. The frequency of c allele was 20% and 3.0% in rs662799, rs3135506, respectively. The GLM model suggested that the SNP rs662799 has significant association with TGL(P < 0.01); there was, however no interaction between gene polymorphisms and food. Also, the prediction model revealed that those who had a carrier allele (C) had higher TGL level as compared with those with wild type (165 vs. 138 mg/dL) and girls had higher TGL levels compared with boys.Conclusion Children with carrier allele of APOA5 are prone to hypertriglyceridemia, irrespective of diet or drugs. These children require periodic monitoring of lipid parameters and effective interventions to prevent the development of atherogenic or metabolic complications.Disclosures All authors: No reported disclosures.

Association of Voltage-Gated Sodium Channel Genetic Polymorphisms with Oxaliplatin-Induced Chronic Peripheral Neuropathy in South Indian Cancer Patients

Oxaliplatin is a platinum drug active against digestive tract cancers. Among its side effects, peripheral neuropathy is one of the dose-limiting toxicities. This affects around 50 to 70% of patients but the pathophysiology of development of oxaliplatin-induced peripheral neuropathy (OXAIPN) remains unclear. Sodium channels (SCNAs) play major role in neuronal electrical signaling processes and mutations in SCNAs lead to various neuronal diseases involving the central and peripheral nervous systems. In this study, we evaluated whether SCNA genetic variants might be associated with risk of chronic OXAIPN in patients with digestive tract cancers treated with oxaliplatin.Methodology:Blood samples from 228 digestive tract cancer patients who had received oxaliplatin in adjuvant and neoadjuvant or metastatic settings were obtained and genomic DNA was extracted by phenol-chloroform extraction. Genotyping was performed with the real-time polymerase chain reaction (RT-PCR) using validated real-time TaqMan single nucleotide polymorphism (SNP) genotyping assays. Neuropathy was evaluated and graded according to National Cancer Institute Common Toxicity Criteria (NCI-CTC) version 4.03.Results:We found that the rs6746030 polymorphic variant of SCN9A was significantly associated with a higher incidence of chronic OXAIPN (GA+AA vs GG: OR=1.8, 95% CI=1.04-3.4, P=0.04; dominant model) while the rs6754031 variant was linked with a lower incidence (OR=0.45, 95% CI=0.22-0.77, P=0.005; dominant model). The SCN 10A polymorphic variant was associated with severity of chronic OXAIPN (P=0.006, OR=2.0, 95% CI=1.2 - 3.3).Conclusion:The results of the present prospective study provide evidence in support of a causal relationship between chronic OXAIPN and voltage gated sodium channel polymorphisms. However, further studies from independent groups are required to validate these results.

Prevalence of IFNL3 gene polymorphism among blood donors and its relation to genomic profile of ancestry in Brazil

The recent development of interferon-free regimens based on direct-acting antivirals for the treatment of chronic hepatitis C virus infection has benefited many but not all patients. Some patients still experience treatment failure, possibly attributed to unknown host and viral factors, such as IFNL3 gene polymorphism. The present study assessed the prevalence of rs12979860-CC, rs12979860-CT, and rs12979860-TT genotypes of the IFNL3 gene, and its relationship with ancestry informative markers in 949 adult Brazilian healthy blood donors. Race was analyzed using ancestry informative markers as a surrogate for ancestry. IFNL3 gene was genotyped using the ABI TaqMan single nucleotide polymorphisms genotyping assays. The overall frequency of rs12979860-CC genotype was 36.9%. The contribution of African ancestry was significantly higher among donors from the northeast region in relation to southeast donors, whereas the influence of European ancestry was significantly higher in southeast donors. Donors with rs12979860-CC and rs12979860-CT genotypes had similar ancestry background. The contribution of African ancestry was higher among rs12979860-TT genotype donors in comparison to both rs12979860-CC and rs12979860-CT genotypes. The prevalence of rs12979860-CC genotype is similar to that found in the US, despite the Brazilian ancestry informative markers admixture. However, in terms of ancestry, rs12979860-CT genotype was much closer to rs12979860-CC individuals than to rs12979860-TT.

Role of polymorphic bile salt export pump (BSEP, ABCB11) transporters in anti-tuberculosis drug-induced liver injury in a Chinese cohort.

Evidence indicates that the polymorphisms in bile salt export pump (BSEP, encoded by ABCB11) may play an important role in the development of anti-tuberculosis drug-induced liver injury (ATDILI) and we aim to investigate the association between genetic variants of ABCB11 and the risk of ATDILI in a Chinese cohort. A total of 89 tuberculosis patients with ATDILI and 356 matched ATDILI -free patients constituted cases and controls. Genetic polymorphisms of ABCB11 were determined by TaqMan single-nucleotide polymorphism (SNP) genotyping assay. Odds ratio (OR) with 95% confidence intervals (CIs) was estimated by conditional logistic regression model. There were no significant differences in genotype frequencies of ABCB11 between cases and controls. In the subgroup analysis, polymorphisms of rs2287616 were found to be associated with cholestatic/mixed pattern of liver injury under dominant and addictive model (OR = 3.84, 95% CI:1.16–12.75, P = 0.028 and OR = 2.51, 95% CI:1.12–5.62, P = 0.025, respectively), however the significance disappeared after Bonferroni correction. This study suggested that genetic variants of ABCB11 gene might contribute to anti-tuberculosis drug-induced cholestatic liver injury in Chinese patients. Studies in larger, varied populations are required to confirm these findings.

CYP7A1, BAAT and UGT1A1 polymorphisms and susceptibility to anti-tuberculosis drug-induced hepatotoxicity.

Evidence indicates that the polymorphisms in genes involved in bile acid metabolism may play an important role in the development of anti-tuberculosis drug-induced hepatotoxicity (ATDH) in tuberculosis (TB) patients treated with anti-tuberculosis drugs. To investigate the association between genetic variants of CYP7A1, BAAT and UGT1A1 and the risk of ATDH in a Chinese cohort. In this nested case-control study, 89 TB patients with ATDH and 356 matched ATDH-free TB patients constituted cases and controls, respectively. Genetic polymorphisms of CYP7A1, BAAT and UGT1A1 were determined using the TaqMan single-nucleotide polymorphism genotyping assay. Odds ratios (ORs) with 95% confidence intervals (CIs) were estimated using a conditional logistic regression model. Significant differences were found in genotype distributions of rs1457043 in CYP7A1 between patients with and those without ATDH (P = 0.014). Genotype and haplotype analysis showed that patients carrying an AG genotype of rs1457043 and G-C or G-A haplotypes of rs1457043-rs8192870 in CYP7A1 were at a higher risk of ATDH than those with GG genotype and A-C haplotype, with ORs of respectively 2.05 (95%CI 1.18-3.15) and 2.40 (95%CI 1.62-3.57). Genetic polymorphisms of CYP7A1 may be associated with susceptibility to ATDH in the Chinese population.

Detection of β-Thalassemia Mutations Using TaqMan Single Nucleotide Polymorphism Genotyping Assays.

Sickle-cell anemia and β-thalassemia are two of the most common autosomal recessive disorders in the developing world. The severity of the problem and the pressure it exerts on the health services in the Kingdom of Saudi Arabia forced the introduction of a national premarital screening program to lessen its impact on the society. Furthermore, a significant effort has been exerted in the elucidation of the genetic causes of such diseases to facilitate diagnosis and detection of carriers. We have designed and validated the use of custom TaqMan(®) genotyping assays for the rapid detection of IVS-I-1 (G>A), IVS-I-5 (G>C), codon 39 (C>T), and IVS-I-110 (G>A) mutations in transfusion-dependent β-thalassemia patients' cohort. We demonstrated that IVS-I-5 (rs33915217) is the most common single-nucleotide variant in our cohort, with the variant allele constituting 26% of the total alleles investigated. However, this variant was not found in 352 alleles screened from buccal swab DNA obtained from healthy volunteers. The TaqMan single nucleotide polymorphism (SNP) genotyping assays are a rapid, accurate, and cost-effective method for the initial screening of β-thalassemia cases, which will minimize the need for direct sequencing of the HBB gene, thus reducing detection costs and increasing throughput.

Association of copy number polymorphisms at the promoter and translated region of COMT with Japanese patients with schizophrenia

Chromosome 22q11.2 deletion syndrome and genetic variations including single-nucleotide polymorphism (SNP) and copy number variation (CNV) in catechol-O-methyltransferase (COMT) situated at 22q11.2 remains controversial. Here, the genetic relationship between COMT and Japanese patients with schizophrenia was investigated by examining whether the SNPs correlated with schizophrenia based on a common disease-common variant hypothesis. Additionally, 22q11.2DS were screened based on a common disease-rare variant hypothesis; low-frequency CNVs situated at two COMT promoters and exons were investigated based on the low-frequency variants with an intermediate effect; and positive findings from the first stage were reconfirmed using a second-stage replication study including a larger sample size. Eight SNPs and 10 CNVs were investigated using Taqman SNP and CNV quantitative real-time polymerase chain reaction method. For the first-stage analysis, 513 unrelated Japanese patients with schizophrenia and 705 healthy controls were examined. For the second-stage replication study, positive findings from the first stage were further investigated using a larger sample size, namely 1,854 patients with schizophrenia and 2,137 controls. The first-stage analysis showed significant associations among schizophrenia, intronic SNP rs165774, CNV6 situated at promoter 1, CNV8 at exon 6, and CNV9 at exon 7. The second-stage study showed that intronic SNP rs165774 (χ(2) = 8.327, P = 0.0039), CNV6 (χ(2) = 19.66, P = 0.00005), and CNV8 (χ(2) = 16.57, P = 0.00025) were significantly associated with schizophrenia. Large and rare CNVs as well as low-frequency CNVs and relatively small CNVs, namely <30 kb in COMT, may be genetic risk factors for schizophrenia.