Influence Of Single Nucleotide Polymorphisms Research Articles

Influence of single nucleotide polymorphisms (SNPs) in genetic susceptibility towards periprosthetic osteolysis.

Wear debris-induced inflammatory osteolysis remains a significant limiting factor for implant replacement surgeries. Hence, a comprehensive understanding of the complex network of cellular and molecular signals leading to these inflammatory responses is required. Both macrophages and monocytes have a critical role in the instigation of the inflammatory reaction to wear debris but differ in the extent to which they induce cytokine expression in patients. Lately, single nucleotide polymorphisms (SNPs) have been associated with genetic susceptibility among individual patients with implant failure. Studies have shown that SNPs in key pro-inflammatory cytokines and their receptors are associated with osteolytic susceptibility. Likewise, SNPs within several genes involved in the regulation of bone turnover have also been found to be associated with wear debris induced osteolysis. It is presumed that SNP variance might play a decisive role in the activation and signaling of macrophages, osteoblasts, chondrocytes, fibroblasts and other cells involved in inflammatory bone loss. Understanding the extent to which SNPs exist among genes that are responsible for inflammatory bone loss may provide potential targets for developing future therapeutic interventions. Herein, we attempt to summarize the various susceptible genes with possible SNP variance that could contribute to the severity of periprosthetic osteolysis in patients with implants.

Association of Neuropeptide S Receptor 1 and Glutamate Decarboxylase 1 Gene Polymorphisms with Posttraumatic Stress Disorder.

Posttraumatic stress disorder (PTSD) is an anxiety disorder caused by highly traumatic experiences. The aim of this study was to investigate the influence of single nucleotide polymorphisms (SNPs) in the neuropeptide S receptor 1 (NPSR1) and the glutamate decarboxylase 1(GAD1) gene on PTSD and its psychopathological aspects among individuals affected by the Balkan wars during the 90s. This study was conducted as part of the South Eastern Europe (SEE) study on molecular mechanisms of PTSD. It comprised 719 participants (539 males), including those with current PTSD, remitted PTSD and healthy volunteers. Psychometric evaluation was performed using the Mini International Neuropsychiatric Interview (M.I.N.I.), the Clinician Administrated PTSD Scale (CAPS) andthe Brief Symptom Inventory (BSI). We examined NPSR1 single nucleotide polymorphism (SNP) rs324981 and GAD1 variant rs3749034 genotypes. Case-control analyses were carried out using logistical regression to determine genotype differences between all patients that had either current or remitted PTSD and control individuals. To analyse the influence of the analysed SNPs on PTSD severity, we performed linear regression analyses with CAPS and BSI within each of the two patient groups separately. All of the calculations were performed for additive allelic, recessive, dominant and genotypic models. We observed a nominally significant association for the major allele (G) of GAD1 rs3749034 with an increased risk to develop PTSD in a case control analysis in the recessive model (P=0.0315, odds ratio=0.47, SE=0.35). In contrast, a nominally significant association of the minor allele (A) with higher CAPS scores was identified within the patient group with lifetime PTSD in the dominant model (P=0.0372, β=6.29, SE=2.99). None of these results did withstand correction for multiple tests. No nominal significant results of GAD1 rs3749034 were found with regard to the intensity of psychological BSI symptoms. Case-control analyses of NPSR1 rs324981 revealed a nominally significant higher risk for homozygous T allele carriers to develop PTSD (P=0.0452) in the recessive model. On the other hand, the T allele showed a nominally significant association with higher BSI scores in patients suffering from lifetime PTSD in the recessive model (P=0.0434). Again, these results were not significant anymore after correction for multiple tests. No associations of NPSR1 rs324981 and CAPS score was identified. The findings of this study provide some evidence that the NPSR1 and GAD1 polymorphisms might play a role in the development of war-related PTSD and its related psychological expressions. Further research is needed to elucidate the interactions of specific gene variants and environmental factors in the development of PTSD.

Atg7 Knockdown Reduces Chemerin Secretion in Murine Adipocytes.

In individuals with obesity, adipocyte endocrine function is affected by altered autophagy. Genetic variants in autophagy-related gene 7 (ATG7) correlated with serum chemerin (RARRES2) concentrations. To investigate a functional interplay between chemerin and ATG7, how it may relate to autophagy-mediated adipocyte dysfunction in obesity, and the relevance of genetic ATG7 variants in chemerin physiology. Adipose ATG7 mRNA expression and adiposity measures were available in two human study cohorts. The effect of a high-calorie diet on adipose Rarres2 and Atg7 expression was investigated in mice. In 3T3-L1 adipocytes, the effect of Atg7 knockdown on chemerin expression and secretion was studied. The influence of single nucleotide polymorphisms on ATG7 transcription and chemerin physiology was investigated using a luciferase assay. Mouse model, clinical trials, in vitro studies. Native American (n = 83) and white (n = 100) cohorts. Adipocyte chemerin expression and secretion. In mice fed a high-calorie diet, adipose Atg7 mRNA expression did not parallel an increase in Rarres2 mRNA expression. ATG7 mRNA expression in human subcutaneous adipose tissue correlated with body mass index, fat mass (r > 0.27; P < 0.01), and adipocyte cell size (r > 0.24; P < 0.02). Atg7 knockdown in 3T3-L1 adipocytes decreased chemerin secretion by 22% (P < 0.04). Rs2606729 in ATG7 was predicted to alter ATG7 transcription and induced higher luciferase activity in vitro (P < 0.0001). Human adipose ATG7 mRNA expression relates to measures of adiposity. Atg7 knockdown reduces chemerin secretion from adipocytes in vitro, supportive of a functional interplay between ATG7 and chemerin in autophagy-mediated adipocyte dysfunction.

PB2402 BETA‐GLOBIN GENE CLUSTER HAPLOTYPES ASSOCIATED WITH HBF VARIATION IN β‐THALASSEMIA CARRIERS OF PORTUGUESE ORIGIN

Background:Genetic association studies showed that HbF levels variation in haemoglobinopathies, such as sickle cell disease and β‐thalassemia (β‐thal), are under the influence of single nucleotide polymorphisms (SNPs) in several genomic loci. The first described polymorphism influencing gamma globin gene expression was XmnI in HBG2 promoter −158C &gt; T (rs7482144). Several reports showed that β‐thal carriers with HbF raised levels have a significantly higher rs7482144 minor allele frequency than patients with low HbF levels. The functional significance of HBG2‐XmnI mutation has never been clearly defined and it is possible that it reflects a marker in linkage disequilibrium (LD) with other functional polymorphism elsewhere in the β‐globin gene cluster. It has been suggested that the role assigned to XmnI could be played by the rs16912979 A &gt; G polymorphism in the palindromic region of 5′HS4 β‐globin locus control region (Neishabury et al., Blood Cells Mol Dis. 2012;48:1‐5).Aims:The main goal of this work was to define haplotype backgrounds in β‐globin gene cluster that could explain HbF variation in a population sample of β‐thal carriers.Methods:We studied 79 Portuguese β‐thal carriers (39 males, 40 females), aged between 2 to 70 years old, with HbF levels ranging from 0.2% to 5.1%. HbA2 levels were 3.4 to 5.8% (mean 4.71). Six different HBB mutations were identified at heterozygous state, the two most commons were c.92+6T &gt; C [IVSI‐6 (T &gt; C)] (n = 30) and c.118C &gt; T [CD39 CAG &gt; TAG)] (n = 23). The remaining mutations were c.48G &gt; A [CD15 TGG &gt; TGA] (n = 11), c.92 + 1G &gt; A [IVS‐I‐1 (G &gt; A)] (n = 10), c.93‐21G &gt; A [IVSI‐110 G &gt; A] (n = 3) and c.20delA [CD 6 ‐A] (n = 2). HbA2 and HbF levels were determined by HPLC. The two SNPs rs16912979 and rs7482144 were genotyped by PCR‐RFLP and the HBB gene mutations were identified by Sanger sequencing. Associations of SNPs with HbF levels were assessed by linear regression models using PLINK. Informed consent was provided by all the participants.Results:The two SNPs HBG2‐XmnI rs7482144 and 5′HS4 rs16912979 were in moderate LD (r2 = 0.65): from a total of 41 rs16912979 G alleles, 73.2% were linked to an rs7482144 T‐allele. Linear regression, in the additive model, showed significant association between the XmnI rs7482144 minor T‐allele and increased levels of HbF (β = 0.648; P = 0.0004). A marginal association was found between the 5’HS4 rs16912979 minor G‐allele and HbF (β = 0.648; P = 0.039), however, no significant association was found after conditioning on XmnI rs7482144 (P = 0.192). The common mutation HBB: c.118C &gt; T [CD39] was found strongly associated with increased levels of HbF (β = 0.948; P = 6.4e‐5), remaining significant after conditional analysis on XmnI rs7482144 (P = 0.0002). Haplotypes combining the HbF‐associated alleles on SNPs rs16912979 and rs7482144 (haplotype GT) showed a significant association with raised levels of HbF (P = 0.0008), explaining 13.7% of HbF levels variation. Combining rs16912979, rs7482144 and mutation HBB: c.118T, three haplotypes were found significantly associated with HbF: GTT (β = 1.346; P = 0.00089), ACT (β = 0.784; P = 0.017) and GTC (β = 0.492; P = 0.032), explaining 13.4%, 7.2% and 5.9% of HbF levels variance, respectively.Summary/Conclusion:Our data suggest that in Portuguese β‐thal carriers the HBG2‐XmnI polymorphism and HBB: c.118C &gt; T [CD39] mutation are associated with HbF levels, showing independent effects. The marginally significant effect on HbF levels variation of SNP 5’HS4 rs16912979 appear to be mediated by the effect of XmnI polymorphism.

Reduced Frequency and Prognostic Significance of Ring Finger Protein 43 Nucleotide Polymorphisms in a Chinese Colorectal Cancer Cohort.

The aim of this research was to verify the mutation rate of the ring finger protein 43 (RNF43) of the transmembrane E3 ubiquitin ligase and investigate the influence of single nucleotide polymorphisms (SNPs) rs2257205 in RNF43 in a Chinese colorectal cancer (CRC) cohort. DNA from 177 diagnosed CRC patients' tissues or blood samples were extracted, amplified, and sequenced. Clinicopathological features, including age, gender, tumor location, tumor-lymph node-metastasis stage, and survival information, were analyzed. Four novel RNF43 mutations (including G659 and R117 sites) were validated in 177 CRC patients; all events were somatic frameshift mutations. Furthermore, we also found that an SNP (rs2257205) of the RNF43 X117 site was associated with overall survival (OS) instead of disease-free survival. G homozygote subjects were significantly correlated with poor OS compared with another group. Then we rescued RNF43 R117R (encoded by nucleotide CGC) and R117H (encoded by nucleotide CAC) expression in the HCT116 cells and analyzed the targets of the Wnt/β-catenin pathway. The expression of CCND1 and c-Myc were decreased. The prognosis of CRC patients could be affected by the different functions of SNPs of RNF43.

Influence of single-nucleotide polymorphisms in the IFNG towards susceptibility to tuberculosis in a Pakistani population.

Tuberculosis (TB) is a global issue as one-third of the population worldwide is considered to be infected. TB has become a critical public health problem as a result of increasing drug resistance, which poses a challenge to current control strategies. Similar to environmental factors, genetic makeup of the host equally contributes to disease onset. We performed genotypic analysis to examine the relationship between IFNG and TB onset and drug resistance in a Pakistani population comprising 689 subjects. Notable differences were observed in the IFNG polymorphism (+874T/A) between the case and control groups. The frequency of the wild-type genotype (TT) in the controls (43.2%) was significantly higher than in the cases (25.3%) (odds ratio [OR] =0.77, p<0.0001), while the mutant genotype frequency (AA) (38.57%) in the cases was significantly higher than in the controls (22.6%) (OR=1.46, p<0.0001). The heterozygous genotype frequency (TA) did not significantly differ between the control and case groups. Compared with the controls, the variant allele (A) was approximately twice as frequent in the cases. Females and older people have a higher chance of disease development. Finally, the IFNG (+874T/A) polymorphism was not associated with drug sensitivity or resistance. However, a genotypic polymorphism of IFNG (+874T/A) was significantly associated with susceptibility to TB, and the T allele conferred protection against TB. Additional studies involving larger cohorts are needed to further explore this relationship between genetics and disease vulnerability.

CALCA and TRPV1 genes polymorphisms are related to a good outcome in female chronic migraine patients treated with OnabotulinumtoxinA

BackgroundSome variables have been proposed as predictors of efficacy of OnabotulinumtoxinA in chronic migraine patients, but data available are inconclusive. We aimed to analyse the influence of single nucleotide polymorphisms in the response to OnabotulinumtoxinA.MethodsWe included 156 female patients treated with OnabotulinumtoxinA accordingly to PREEMPT paradigm in three headache units. OnabotulinumtoxinA was offered to patients that had not responded to topiramate and at least one other preventative. Age at first procedure was 43.7 ± 11.8 years (16–74). Patients with a reduction of at least 50% in the number of migraine days after two OnabotulinumtoxinA procedures were considered as responders. We analysed 25 polymorphisms selected for their relevance regarding migraine pathophysiology and their association with migraine according to previously published genome-wide association studies. Genotyping was performed using KASP probes and a LightCycler-480 (Roche-Diagnostics). Allelic, genotypic frequencies and dominance/recesivity hypothesis of the allelic variants were compared between responders and non-responders by Fisher’s exact test.ResultsResponse to treatment with OnabotulinumtoxinA was achieved in 120 patients (76,9%). Two polymorphisms showed differences: CALCA rs3781719, where allele C represents 26.9% in responders and 40.9% in non-responders (p = 0.007, OR = 3.11 (1.33–7.26)); and TRPV1 rs222749, where allele A represents 4.17% in responders and 12.5% in non-responders (p = 0.013, OR = 3.29 (1.28–8.43)). No significant differences in rest of polymorphisms or clinical or demographic variables were found.ConclusionsPolymorphic variations of CALCA and TRPV1 genes might play a role as prognostic markers of efficacy of OnabotulinumtoxinA in chronic migraine female patients in our population.

(122) S100B Single Nucleotide Polymorphisms and Haplotypes Associate with Both Acute Crisis Pain and Chronic Pain in Sickle Cell Disease

Pain in sickle cell disease (SCD) is complex and heterogeneous. In this study, we examine the influence of single nucleotide polymorphisms (SNP) in the S100B gene on acute and chronic pain variation in SCD. 136 subjects with SCD recorded their baseline, non-crisis pain experience on a digital version of the McGill Pain Questionnaire, from which we obtained composite pain index (CPI) scores as a measurement for chronic pain. Utilization of emergency or urgent care owing to painful crisis was recorded as a marker for acute pain. Blood/buccal swab samples were collected and genotyped using MassARRAY iPLEX platform. Multiple linear regression analyses revealed association with higher CPI scores for rs9983698 T allele (additive: B= 4.91, p= 0.014; dominant: B= 6.43, p= 0.009), rs9722 A allele (additive: B= 4.81, p= 0.005; dominant: B= 7.80, p= 0.003), and rs11911834 T allele (additive: B= 4.75, p= 0.016; dominant: B= 6.13, p= 0.011). On the other hand, the G allele of rs1051169 associated with decreased CPI (additive: B= -6.14, p= 0.001; dominant: B= -6.56, p= 0.009; recessive: B= -9.78, p= 0.005). Further, ordinal logistic regression of utilization groups showed that the G allele of rs1051169 also associated with lower utilization (additive: B= -1.02, p= 0.0003; dominant: B= -1.20, p= 0.002; recessive: B= -1.26, p= 0.015). Employing linkage disequilibrium plot, we identified two haploblocks for these 4 SNPs. In block 1 (rs9983698-rs9722), haplotypes T-A and C-G significantly associated with CPI (B= 5.63, -4.81; p= 0.007, 0.005, respectively). In block 2 (rs1051169-rs11911834), C-T and G-G haplotypes showed significant association with CPI (B= 4.52, -6.02; p= 0.024, 0.001, respectively). S100B SNPs and haplotypes were found to associate with acute and chronic pain in SCD indicating the potential role of S100B in sickle cell pain heterogeneity. Supported by grants from the NIH (R01HL124945, R01HL098141, T32DE018381) and IDPH.

Influence of IL-1R2 polymorphisms on endometrial cancer susceptibility in the Chinese Han population.

BackgroundRecently, many studies have identified that genetic factor plays a crucial role in endometrial cancer development. The purpose of this study is to investigate the influence of single nucleotide polymorphisms (SNPs) of IL‐1R2 on endometrial cancer susceptibility.MethodsWe performed a case‐control study that included 293 patients with endometrial cancer and 579 healthy controls. Six SNPs in the IL‐1R2 gene were genotyped using the Agena MassARRAY platform. Genetic models and haplotype analyses were used to assess the association between SNPs and endometrial cancer risk by computing odds ratios (ORs) and 95% confidence intervals (CIs).ResultsOverall analysis results found that two SNPs (rs4851527 and rs3218896) and haplotypes TGTC and TACT were significantly associated with endometrial cancer risk. Stratified analysis by age showed that rs2072472 was associated with endometrial cancer risk in age >54 subgroup.ConclusionsThese findings suggested that IL‐1R2 polymorphisms may contribute to the development of endometrial cancer. Further studies are required to confirm the results.

Role of THRB, ARG1, and ADRB2 Genetic Variants on Bronchodilators Response in Asthmatic Children.

Background: An interindividual variability in response to short-acting bronchodilator drugs (short-acting inhaled β2-agonists, SABA) exists and this is linked in part to genetic factors. The aim of this study was to verify the influence of single nucleotide polymorphisms (SNPs) of a previously studied gene (ADRB2) and of new candidate genes (THRB and ARG1) on the acute response to SABA in children with asthma. Methods: One hundred asthmatic children (mean age 9.6 ± 3.0 years, 77 boys) underwent allergological and lung function evaluations. Spirometry was performed before and after bronchodilation test (BD test). The ADRB2 region containing the Arg16Gly (rs1042713) and Gln27Glu (rs1042714) variants were amplified by polymerase chain reaction, whereas ARG1 rs2781659 (A>G) and THRB rs892940 (G>A) SNPs were genotyped by high-resolution melting (HRM) analysis. Results: Seventy-seven percent of children developed asthma in the first 6 years of life. Allergic sensitization was observed in 92% (total immunoglobulin G: 529.8 ± 477. kU/L). All patients exhibited respiratory allergy: 43% has multiple respiratory, 22% to single respiratory, and 27% multiple respiratory and food allergies. Fifty four percent children showed positive BD response (forced expiratory volume in 1 second [FEV1] > 12%). Presence of Arg/Gly or Gly/Gly genotypes in position 16 of ADRB2 was significantly associated to a worse BD response (post-BD FEV1: 108.68% ± 15.62% in Arg/Arg vs. 101.86% ± 14.03% in Arg/Gly or Gly/Gly patients, p = 0.02). No significant association was found between spirometric parameters before and after BD for the other three examined SNPs. Conclusion: The influence of genetic variability on responsiveness to drugs could become a key parameter to optimize a tailored therapy for young patients with asthma, especially if drug-resistance occurs.

The combined polymorphisms of interleukin-6-174GG genotype and interleukin-10 ATA haplotype are associated with a poor quality of life in patients with chronic hepatitis C.

Chronic hepatitis C (CHC) is associated with a decreased health-related quality of life (HRQOL). More recent studies have pointed toward a genetic basis of patient-reported quality of life outcomes. Taking into account that the influence of single-nucleotide polymorphisms (SNPs) on the HRQOL of CHC patients has not been studied, we investigated the combined IL10-1082G/A, - 819C/T, and - 592C/A SNPs, and IL6-174G/C SNP. We also evaluated the association between demographic, clinical, psychiatric, virological, and genetic variables with domains and summaries of HRQOL in CHC patients. 132 consecutive CHC patients and 98 controls underwent psychiatric evaluation by using the Mini International Neuropsychiatric Interview. HRQOL was assessed by a generic questionnaire, the Medical Outcomes Study 36-Item Short Form Health Survey (SF-36), and by the specific Liver Disease Quality of Life Questionnaire (LDQOL). IL6 and IL10 polymorphisms were evaluated by Taqman SNP genotyping assay. Multivariate analysis was used to evaluate the associations. Major depressive disorder was associated with lower SF-36 and LDQOL scores in seven and ten domains, respectively. Diabetes and hypertension were also associated with reduced HRQOL. CHC patients carrying the combination of IL10 ATA haplotype/IL6-GG genotype had lower scores in the SF-36-physical functioning domain, and reduced scores in the LDQOL effects of liver disease on activities of daily living, quality of social interaction, and sexual function domains than the non-carriers of the combined haplotype/genotype. This is the first study to demonstrate that combined IL6 high-producer GG genotype and IL10 low-producer ATA haplotype is associated with poorer HRQOL in CHC patients.

Influence of single nucleotide polymorphism of Wilms tumor 1 gene on the efficacy and clinical prognosis of elderly patients with acute myeloid leukemia

Objective To evaluate the influence of single nucleotide polymorphism of Wilms tumor 1(WT1)gene rs16754 on the chemosensitivity and clinical outcomes of elderly patients with acute myeloid leukemia(AML). Methods A total of 178 AML patients aged 60 years and over who received cytarabine-based chemotherapy were enrolled in this retrospective study.The peripheral blood was extracted from 178 AML patients receiving chemotherapy for DNA preparation and study.And bone marrow specimens were collected in 65 AML patients before chemotherapy.The Wilms' Tumor-1(WT1)rs16754 polymorphism was detected by PCR-RFLP method.The association between genotypes and other variables were analyzed by using Logistic regression model.Variables were adjusted by Cox regression analysis. Results The locus of WT1 gene rs16754 is located in coding region of WT1 gene.The genotype frequency and distribution of the studied population were 55.62%(99/178)in GG, 37.64%(67/178)in GA, and 6.74%(12/178)in AA, with minimum allele frequencies of 0.26.The distributions of the three genotypes were in accordance with Hardy-Weinberg Equilibrium(P=0.884). There was no statistical difference in the data distribution of the genotypes on clinical indexes at baseline.Overall survival time(OS)was longer in patients with allele A and genotype GA plus AA[2.73 years(95%CI: 1.03-5.11 years)]than in patients with GG genotype[1.64 years(95%CI: 0.71-4.34), (P=0.003)]. The replase free survival(RFS)was longer in patients with allele A and genotype GA plus AA[2.06 years(95%CI: 0.95-4.87)]than in patients with GG genotype[1.12 years(95%CI: 0.56-4.11), P=0.032)]. Adjusted by using multivariate Cox regression analysis, GA plus AA genotypes still showed a better effect on OS(HR=0.51, P=0.013)than did GG genotypes.In the 65 pretreatment bone marrow specimens, the expression level of WT1 mRNA in bone marrow cells was higher in patients with GG genotype than in patients with GA plus AA genotype(P<0.001). Conclusions Among elderly AML patients treated by cytarabine-based chemotherapy, the WT1 rs16754 may impact the clinical prognosis of AML patients by influencing the mRNA expression of WT1. Key words: Leukemia, myeloid; Polymorphism, single nucleotide; Treatment outcome

Genetic Variations Hasten Decline in Young Onset Dementia

Aims There is increasing interest in the influence of single nucleotide polymorphisms (SNPs) on the trajectory of cognitive decline in dementia. We evaluated the hypothesis that rs1768208 risk allele copies are associated with cognitive decline in behavioral variant frontotemporal degeneration (bvFTD), a common form of young-onset dementia. Methods Forty-three individuals diagnosed with bvFTD (mean baseline age=60.1 years ±7.7, mean disease duration at baseline 3.6 years ± 2.2, mean baseline MMSE 26.2 years ± 7.1) were studied. All subjects had at least 2 verbal fluency observations to assess executive function. Patients were genotyped for rs1768208 using a custom pan-neurodegenerative disease SNP genotyping panel and were coded according to the number of risk (T) alleles (0,1,2). Linear mixed-effects models assessed the effect of genotype on performance changes over time. To evaluate the neuroanatomic basis for longitudinal decline, regression analyses related performance change in executive function to grey matter (GM) and white matter (WM). Results There was a significant dose-dependent genotype by time interaction (F[2, 29]=8.42; p=0.001) for declining performance on verbal fluency (B values refer to words per month): 2 risk alleles (B=0.48; p Conclusions Individuals with rs1768208 risk alleles are at risk for a rapid decline in executive function and this is related to more severe neurodegeneration in key frontal regions. These findings suggest that individual genetic variations contribute to heterogeneity in clinical progression.

Pharmacogenomics of Methotrexate: Current Status and Future Outlook.

Methotrexate (MTX) is a folate analogue with high therapeutic efficiency in the treatment of cancers and autoimmune diseases. The efficacy and toxicity of MTX may be altered by genetic polymorphisms in genes involved in MTX metabolic pathway. Personalized pharmacotherapy based on gene polymorphisms enables a more efficient, compatible and cost-effective treatment of patients. The present article aims to review genetic polymorphisms associated with MTX pharmacokinetics, toxicity, and outcome, and points out future development directions of individualized MTX therapy. Details regarding the pharmacogenetics and pharmacogenomics of MTX are obtained from PubMed literatures. The influences of single nucleotide polymorphisms (SNPs) in genes involved in MTX pathway are controversial. Many pharmacogenetic associations are disease specific and race specific. Present studies have almost limited to some certain ethnic groups and diseases. The data from these studies are not convincing enough to draw far-reaching conclusions about the applicability of MTX pharmacogenetics in clinical practice. Studies with large scale and multiple centers are needed in the future. MTX-PG inhibits folic metabolism through three mechanisms. TS, MTHFR and ATIC are the rate-limiting enzymes separately. The function of SNPs in these genes is often onesided. Works focusing on the analysis of polymorphism in MTX transporters should be more efficient and meaningful.

Influence of single nucleotide polymorphism in IL-27 and IL-33 genes on breast cancer

Breast cancer is a common disease in women, and is increasing in frequency in both developed and developing countries [1]. Although the main cause is, as yet, fully established, aetiology is likely...

Lack of effect of the SLC47A1 and SLC47A2 gene polymorphisms on the glycemic response to metformin in type 2 diabetes mellitus patients.

Background This work aimed to evaluate the influence of single nucleotide polymorphisms (SNPs) in the SLC47A1 (922-158G>A; rs2289669) and SLC47A2 (-130G>A; rs12943590) genes on the relative change in HbA1c in type 2 diabetes mellitus (T2DM) patients of South India who are taking metformin as monotherapy. It also aims to study the effects of these SNPs on the dose requirement of metformin for glycemic control and the adverse effects of metformin. Methods Diabetes patients on metformin monotherapy were recruited based on the eligibility criteria (n=105). DNA was extracted and genotyping was performed with a real-time PCR system using TaqMan® SNP genotyping assay method. The HbA1c levels were measured using Bio-Rad D-10™ Hemoglobin Analyzer. Results After adjusting for multiple comparisons (Bonferroni correction) the difference found in the glycemic response between the "GG" genotype and "AG/AA" genotype groups of the SLC47A2 gene was not significant (p=0.027; which was greater than the critical value of 0.025). Patients with "GG" genotype showed a 5.5% decrease in HbA1c from baseline compared to those with the "AG/AA" genotype (0.1% increase). The SNP in the SLC47A1 gene also did not influence the glycemic response to metformin (p=0.079). The median dose requirements based on the genotypes of the rs12943590 variant (p=0.357) or rs2289669 variant (p=0.580) were not significantly different. Similarly, there was no significant difference in the occurrence of adverse effects across the genotypes in both the SLC47A1 (p=0.615) and SLC47A2 (p=0.309) genes. Conclusions The clinical response to metformin was not associated with the SNPs in the SLC47A1 and SLC47A2 genes coding for the multidrug and toxin extrusion protein (MATE) transporters. Furthermore, the studied SNPs had no influence on the dose requirement or adverse effects of metformin.

Influence of single nucleotide polymorphisms in pri-miR-124-1 and STAT3 genes on gastric cancer susceptibility

ABSTRACTIntroduction: MicroRNAs (miRNAs) are small ribonucleic acids that modulate the expression of downstream target genes. There is considerable evidence of their involvement in many malignancies, such as oesophageal and gastric. We hypothesised altered expressions of pri-miR-124-1 rs531564 and STAT3 rs1053023 polymorphisms in gastric cancer.Materials and methods: Genomic DNA was extracted from peripheral blood of 250 patients with gastric cancer and 310 healthy individuals. The RFLP method was applied for determination of pri-miR-124 polymorphism and the AS-PCR method for STAT3 polymorphism.Results: The distribution of rs531564 genotypes in cases and controls was different: the G allele carriers had a reduced gastric cancer risk (OR = 0.62; 95%CI = 0.49–0.80, P = 0.0002). Presence of the minor allele of STAT3 (rs1053023) was linked with higher risk of gastric cancer (OR = 2.29; 95% CI = 1.79–2.93, P < 0.0001). Compared with the most frequent haplotype C-G [the SNP order was pri-miR-124-1 (rs531564) and STAT3 (rs1053023)] in controls, C-A haplotype was associated with a significantly increased risk of gastric cancer (OR = 2.28; 95%CI = 1.64–3.09, P < 0.0001).Conclusion: There is a strong link between pri-miR-124-1 rs531564 and STAT3 rs1053023 and gastric cancer that may be pathogenic, and so worthy of further investigation.

Clinicopathological significance of SNPs in RAD51 and XRCC3 in oral and oropharyngeal carcinomas.

This study investigated the influence of single nucleotide polymorphisms (SNP) in RAD51 and XRCC3 on susceptibility to oral and oropharyngeal squamous cell carcinomas (SCC) and determined their clinicopathological significance. SNPs rs1801320 and rs1801321 in RAD51 and rs861539 in XRCC3 were genotyped in 81 patients presenting oral SCC, 45 presenting oropharyngeal SCC, and 130 healthy controls, using TaqMan allelic discrimination assays. Multiple logistic regression models were used to explore the association between SNPs and cancer development, as well as gene-gene (GxG) interaction and gene-environmental factor (GxE) interaction. Clinicopathological associations were verified through the chi-square test, and univariate and multivariate methods were applied for survival analyses. Although allelic and genotypic models and the GxG interaction analysis were nonsignificant, the GxE analysis revealed synergistic effects of the risk alleles of rs1801320, rs1801321, and rs861539 with smoking and alcohol consumption on susceptibility to oral and oropharyngeal SCC. Furthermore, oropharyngeal SCC patients carrying the XRCC3 rs861539 GT/TT genotype (T risk allele) presented a shorter overall survival than GG genotype carriers. Combined effects of RAD51 (rs1801320 and rs1801321) and XRCC3 (rs861539) SNPs with environmental carcinogens (tobacco and alcohol) are associated with oral and oropharyngeal SCC development.

Drug-metabolizing enzymes CYP3A as a link between tacrolimus and vitamin D in renal transplant recipients: is it relevant in clinical practice?

CYP3A enzymes are involved in the metabolism of calcineurin inhibitor tacrolimus as well as vitamin D. In this review, we summarize the clinical aspects of CYP3A-mediated metabolism of tacrolimus and vitamin D with emphasis on the influence of single-nucleotide polymorphisms on tacrolimus disposition. We describe the utility of 4β hydroxycholesterol as a marker of CYP3A activity. Then, we discuss the possible interaction between calcineurin inhibitors and vitamin D in solid organ transplant recipients. Also, we review other mechanisms which may contribute to side effects of calcineurin inhibitors on bone. Lastly, suggestions for future research and clinical perspectives are discussed.

Influence of MBL2 and NOS3 polymorphisms on spontaneous preterm birth in North East Brazil: genetics and preterm birth

Background: The mannose-binding lectin (MBL2) and nitric oxide synthase 3 (NOS3) genes are associated with the immune response against inflammatory processes, have been reported as possibly related with premature birth. Until now, most of the researches regarding the genetic influence of prematurity have revealed limited results because only investigating the child or the mothers’ genotypes, thus not exploring the possible effects of interactions between these genotypes or the interactions with environmental factors related to the duration of pregnancy.Objective: We performed a replica study investigating the influence of single nucleotide polymorphisms (SNPs) in MBL2 and NOS3 genes on premature birth, also considering socioeconomic, demographic, and gestational factors.Materials and methods: We conducted a case–control study with 189 mother–infant dyads, with 104 spontaneous preterm births and 85 term births from Recife, Brazil. We used peripheral blood samples and umbilical cord samples to extract DNA. Functional SNPs at exon 1 and promoter region of MBL2 and NOS3 RS1799983 SNP were genotyped using direct sequencing and fluorescent allelic specific TaqMan® assays respectively. Data were analyzed using the Statistical Package for the Social Sciences (SPSS®) program with bivariate association and logistic multivariate regression tests.Results: We observed a prevalence of MBL2 wild-type genotype in the mother–infant dyad of the preterm group and polymorphic genotype in the mother–infant dyad of term birth. The haplotype LYA predominated in our sample, being more frequent in the preterm group, while the haplotype LYB, correlated with lower levels of MBL protein, was more frequent in the term birth group. About NOS3 RS1799983 SNP, the G/G genotype was more frequent throughout the sample. The heterozygous genotype predominated among women from the preterm group, showed a borderline difference between the groups. When MBL2 genotypes of the mother and son were analyzed together, codon 54 of MBL2 remained associated with prematurity. When the variables with p value lower than .20 in the bivariate analysis were analyzed by logistic regression, the low weight of the pregnant woman in relation to the gestational age, the occurrence of preterm premature rupture of membranes, urinary tract infection during birth and maternal history of other premature births were risk factors to prematurity. On the other hand, the presence of B allele at codon 54 of maternal MBL2 was a protective factor for the occurrence of spontaneous premature birth. In contrast, a borderline association was established between the maternal genetic variation within NOS3 gene and the outcome studied.Conclusions: Our study, limited by the small number of patients enrolled, indicates that MBL2 and NOS3 functional SNPs are associated with the occurrence of spontaneous prematurity and the regulation of the maternal inflammatory response. Despite these results are in agreement with previously reports, our findings do not replicate the ones reported in a large genome-wide association study performed on quite high number of subjects. Thus, we can conclude that MBL2 and NOS3 functional SNPs are plausible candidate risk factors just in few preterm birth cases, and consequently they cannot be included in the general diagnostic practice.