Contribution Of Single Nucleotide Polymorphisms Research Articles

Clinical implications of genetic polymorphisms in blepharospasm.

The possible genetic variants associated with blepharospasm (BSP) and facial dystonia have been investigated. Although genetic variants associated with BSP have been extensively studied, the contribution of single-nucleotide polymorphisms towards this condition remains poorly understood. In addition, the etiology of BSP remains to be fully elucidated. Therefore, the present study aimed to assess the role of polymorphisms in the torsin 1A (TOR1A), dopamine receptor D (DRD)2 and DRD5 genes in South Korean patients with BSP. Furthermore, the role of genetic variants of these three aforementioned genes was investigated. A prospective case-control study was established, where 56 patients with BSP and 115 healthy controls were recruited at the Department of Ophthalmology of CHA Bundang Medical Center (Seongnam, South Korea) using single nucleotide polymorphisms analysis by real-time PCR. The TOR1A rs1182CC/DRD5 rs6283TC genotype combination was found to be associated with decreased BSP risk [adjusted odds ratio (AOR), 0.288; P=0.013]. DRD5 rs6283 was observed to be associated with the periocular type of BSP in the co-dominant (for the TC genotype; AOR, 0.370; P=0.029) and dominant models (AOR, 0.406; P=0.029). The recessive model of TOR1A rs1801968 (AOR, 0.245; P=0.030), and the recessive (AOR, 0.245; P=0.029) and over-dominant models (AOR, 2.437; P=0.019) of DRD2 rs1800497 were found to be associated with superior responses to botulinum neurotoxin A (BoNT) treatment. By contrast, dominant (AOR, 0.205; P=0.034) and additive (AOR, 0.227; P=0.030) models of DRD5 rs6283 were associated with poor responses to BoNT treatment. To conclude, these results suggested that DRD2 rs1800497 can confer genetic susceptibility to BSP responses to BoNT treatment, whereas the TOR1A rs1182CC/DRD5 rs6283TC genotype combination appeared to contribute to the association with BoNT efficacy in BSP.

Thrombospondin-1, BIM and CFH polymorphisms and response to anti-VEGF treatment in neovascular age- related macular degeneration patients.

Age-related macular degeneration (AMD) is a vision threatening disease in older adults. Anti-VEGF treatment is effective for the majority of neovascular AMD (nAMD) patients, although approximately 30% of nAMD patients have an incomplete response for unknown reasons. Here we assessed the contribution of single nucleotide polymorphisms (SNPs) in key angioinflammatory regulatory genes in nAMD patients with an incomplete response compared to those responsive to anti-VEGF treatment. A total of 25 responsive and 30 nAMD patients with an incomplete response to anti-vascular endothelial growth factor (anti-VEGF) treatment were examined for known SNPs that impact the structure and function of thromobospondin-1 (TSP1), Bcl-2-interacting mediator of cell death (BIM) and complement factor H (CFH). Plasma levels of C-C motif chemokine ligand 2 (CCL2/MCP1), TSP1 and VEGF were assessed by ELISA. Patients responsive to anti-VEGF treatment showed a significant increase in the TSP1 rs2228262 AA allele and a trend for the BIM (rs724710) CT allele. Consistent with previous reports, 42% of the patients responsive to anti-VEGF expressed the CC allele for CFH rs1061170. Although the CFH TT allele had similarly low prevalence in both groups, the TC allele tended to be more prevalent in patients with an incomplete response. Patients with an incomplete response also had increased plasma CCL2/MCP1 levels, consistent with the role increased inflammation has in the pathogenesis of nAMD. Our studies point to new tools to assess the potential responsiveness of nAMD patients to anti-VEGF treatment and suggest the potential use of anti-CCL2 for treatment of nAMD patients with an incomplete response to anti-VEGF.

Association between single nucleotide polymorphisms of interleukin-35 genes and atopic dermatitis.

The pathogenesis of atopic dermatitis (AD) involves complex interactions between environmental factors, the skin microbiome, epidermal barrier defects, and altered immune responses that develop on a not fully understood specific genetic background. We aimed to evaluate the contribution of single nucleotide polymorphisms (SNPs) in the IL-35 genes (IL-12A and EBI3) towards AD susceptibility and clinical characteristics of AD in the Polish population. Two SNPs (rs568408, rs582054) in IL-12A and one SNP (rs428253) in EBI3 were selected. Blood samples were collected from 202 AD patients and 178 healthy individuals. SNPs in IL-35 genes were analysed by the polymerase chain reaction with sequence-specific primers (SSP-PCR) method. For IL-12A rs568408, the AA genotype was significantly linked to increased odds of AD (OR = 34.61; 95% CI: 2.06-579.97, p = 0.0137) and marginally associated with normal total serum IgE levels (OR = 2.82; 95% CI: 0.97-8.16; p = 0.05), while the GA genotype showed significantly reduced odds of AD (OR = 0.53; 95% CI: 0.34-0.81; p = 0.0035). In the context of IL-12A rs582054, TT genotype carriers had increased odds of AD (OR = 2.05; 95% CI: 1.08-3.85; p = 0.03). Patients with the GG genotype of EBI3 rs428253 had decreased odds of high total serum IgE levels (OR = 0.42; 95% CI: 0.20-0.86; p = 0.02) and milder pruritus severity compared to CC genotype carriers (4.12 vs. 7.50; p = 0.02). IL-35 genetic variations appear to play a role in AD pathogenesis.

Mitochondrial apoptosis-related gene polymorphisms are associated with responses to anthracycline-based chemotherapy in acute myeloid leukaemia.

Although anthracyclines are the first-line chemotherapy drugs for treating non-M3 acute myeloid leukaemia (AML), their efficacy remains limited. It is important to identify factors that influence the efficacy of anthracyclines against AML. Mitochondrial apoptosis-related genes play significant roles in the pathogenesis, treatment, and prognosis of AML. We utilized the CRISPR/Cas9 screening system to find AML anthracyclines resistance related genes and several mitochondrial apoptosis-related genes, such as BCL2L11, CASP8, TP63, TP53BP2, PLAUR, SOD2, BNIP3L, and MMP9, were screened out. Then, DNA from 279 patients with AML and 321 healthy individuals were extracted and the contributions of single nucleotide polymorphisms (SNPs) within these genes to the patient's chemotherapy response, susceptibility to AML, and overall survival were investigated. Our findings indicated that SNP rs4251864 in the PLAUR gene was associated with an increase in complete remission after anthracycline-based induction chemotherapy. rs4880 in SOD2 was associated with the response to the second course of chemotherapy, whereas rs3789068 in BCL2L11 was associated with susceptibility to AML. Our results about the association of SNPs in mitochondrial apoptosis-related genes with the response to anthracycline-based chemotherapy in AML provide an important reference for predicting the treatment outcomes in patients with this disease.

Risk score prediction model based on single nucleotide polymorphism for predicting malaria: a machine learning approach

BackgroundThe malaria risk prediction is currently limited to using advanced statistical methods, such as time series and cluster analysis on epidemiological data. Nevertheless, machine learning models have been explored to study the complexity of malaria through blood smear images and environmental data. However, to the best of our knowledge, no study analyses the contribution of Single Nucleotide Polymorphisms (SNPs) to malaria using a machine learning model. More specifically, this study aims to quantify an individual's susceptibility to the development of malaria by using risk scores obtained from the cumulative effects of SNPs, known as weighted genetic risk scores (wGRS).ResultsWe proposed an SNP-based feature extraction algorithm that incorporates the susceptibility information of an individual to malaria to generate the feature set. However, it can become computationally expensive for a machine learning model to learn from many SNPs. Therefore, we reduced the feature set by employing the Logistic Regression and Recursive Feature Elimination (LR-RFE) method to select SNPs that improve the efficacy of our model. Next, we calculated the wGRS of the selected feature set, which is used as the model's target variables. Moreover, to compare the performance of the wGRS-only model, we calculated and evaluated the combination of wGRS with genotype frequency (wGRS + GF). Finally, Light Gradient Boosting Machine (LightGBM), eXtreme Gradient Boosting (XGBoost), and Ridge regression algorithms are utilized to establish the machine learning models for malaria risk prediction.ConclusionsOur proposed approach identified SNP rs334 as the most contributing feature with an importance score of 6.224 compared to the baseline, with an importance score of 1.1314. This is an important result as prior studies have proven that rs334 is a major genetic risk factor for malaria. The analysis and comparison of the three machine learning models demonstrated that LightGBM achieves the highest model performance with a Mean Absolute Error (MAE) score of 0.0373. Furthermore, based on wGRS + GF, all models performed significantly better than wGRS alone, in which LightGBM obtained the best performance (0.0033 MAE score).

The oxytocin signalling gene pathway contributes to the association between loneliness and cardiometabolic health

Increasing evidence has shown adverse effects of loneliness on cardiometabolic health. The neuromodulator and hormone oxytocin has traditionally been linked with social cognition and behaviour. However, recent implications of the oxytocin system in energy metabolism and the overrepresentation of metabolic issues in psychiatric illness suggests that oxytocin may represent a mechanism bridging mental and somatic traits. To clarify the role of the oxytocin signalling system in the link between cardiometabolic risk factors and loneliness, we calculated the contribution of single nucleotide polymorphisms (SNPs) in the oxytocin signalling pathway gene-set (154 genes) to the polygenic architecture of loneliness and body mass index (BMI). We investigated the associations of these oxytocin signalling pathway polygenic scores with body composition measured using body magnetic resonance imaging (MRI), bone mineral density (BMD), haematological markers, and blood pressure in a sample of just under half a million adults from the UK Biobank (BMD subsample n = 274,457; body MRI subsample n = 9796). Our analysis revealed significant associations of the oxytocin signalling pathway polygenic score for BMI with abdominal subcutaneous fat tissue, HDL cholesterol, lipoprotein(a), triglycerides, and BMD. We also found an association between the oxytocin signalling pathway polygenic score for loneliness and apolipoprotein A1, the major protein component of HDL. Altogether, these results provide additional evidence for the oxytocin signalling pathway’s role in energy metabolism, lipid homoeostasis, and bone density, and support oxytocin’s complex pleiotropic effects.

Genome-wide association studies in Japanese women identified genetic loci associated with wrinkles and sagging.

Wrinkles and sagging are caused by various factors, such as ultraviolet rays; however, recent findings demonstrated that some individuals are genetically predisposed to these phenotypes of skin aging. The contribution of single nucleotide polymorphisms (SNPs) to the development of wrinkles and sagging has been demonstrated in genome-wide association studies (GWAS). However, these findings were mainly obtained from European and Chinese populations. Limited information is currently available on the involvement of SNPs in the development of wrinkles and sagging in a Japanese population. Therefore, we herein performed GWAS on wrinkles at the outer corners of the eyes and nasolabial folds in 1041 Japanese women. The results obtained revealed that 5 SNPs (19p13.2: rs2303098 (p=3.39 × 10-8 ), rs56391955 (p=3.39 × 10-8 ), rs67560822 (p=3.50 × 10-8 ), rs889126 (p=3.78 × 10-8 ), rs57490083 (p=3.99 × 10-8 )) located within the COL5A3 gene associated with wrinkles at the outer corners of the eyes. Regarding nasolabial folds, 8q24.11 (rs4876369; p=1.05 × 10-7 , rs6980503; p=1.25 × 10-7 , rs61027543; p=1.25 × 10-7 , rs16889363; p=1.38 × 10-7 ) was suggested to be associated with RAD21 gene expression. These SNPs have not been reported in other populations, and were first found in Japanese women population. These SNPs may be used as markers to examine the genetic predisposition of individuals to wrinkles and sagging.

Rs868058 in the Homeobox Gene HLX Contributes to Early-Onset Fetal Growth Restriction.

Simple SummaryFetuses with hypotrophy (FGR, fetal growth restriction) are too small for their gestational age and may be prone to various diseases and loss of life. This study aimed to determine the role of single nucleotide polymorphisms (SNPs), located in two homeotic and two angiogenesis-related genes, in the occurrence of FGR, by analyzing blood samples from 380 women in singleton pregnancies. We found that the AT heterozygotes in HLX rs868058 were significantly associated with an approximately two-fold increased risk of FGR, diagnosed before 32 weeks of gestation (early-onset FGR). AT heterozygotes were significantly more frequent in women with early-onset FGR than in those with late-onset FGR (diagnosed from 32 weeks of gestation) and compared with healthy subjects. In conclusion, the AT genotype in HLX rs868058 may be a significant risk factor for the development of early-onset FGR. So far, the only therapeutic strategy for the management of early-onset FGR is to monitor and terminate pregnancy when the risk of fetal immaturity is lower than the risk of intrauterine death. Therefore, the disclosure of the mechanisms of action of the heterozygous AT state in HLX rs868058 would be important to identify plausible targets for new therapeutic approaches to treat the condition.Fetal growth restriction (FGR) is a condition that characterizes fetuses as too small for their gestational age, with an estimated fetal weight (EFW) below the 10th percentile and abnormal Doppler parameters and/or with EFW below the 3rd percentile. We designed our study to demonstrate the contribution of single nucleotide polymorphisms (SNPs) from DLX3 (rs11656951, rs2278163, and rs10459948), HLX (rs2184658, and 868058), ANGPT2 (−35 G > C), and ITGAV (rs3911238, and rs3768777) genes in maternal blood in FGR. A cohort of 380 women with singleton pregnancies consisted of 190 pregnancies with FGR and 190 healthy full-term controls. A comparison of the pregnancies with an early-onset FGR and healthy subjects showed that the AT heterozygotes in HLX rs868058 were significantly associated with an approximately two-fold increase in disease risk (p ≤ 0.050). The AT heterozygotes in rs868058 were significantly more frequent in the cases with early-onset FGR than in late-onset FGR in the overdominant model (OR 2.08 95% CI 1.11–3.89, p = 0.022), and after being adjusted by anemia, in the codominant model (OR 2.45 95% CI 1.23–4.90, p = 0.034). In conclusion, the heterozygous AT genotype in HLX rs868058 can be considered a significant risk factor for the development of early-onset FGR, regardless of adverse pregnancy outcomes in women.

Association of leptin receptor gene polymorphisms and meta-inflammation markers with metabolically unhealthy obesity in children

The aim: to study the contribution of single-nucleotide polymorphisms (SNP) of the leptin receptor (LEPR) gene and meta-inflammation markers to the formation of metabolically unhealthy obesity (MUO) in children. Materials and methods. A total of 109 obese children aged 6–18 years were examined. Based on the recommendations of the National Heart, Lung, and Blood Institute (NHLBI), 2 observation groups were formed. The main group (n = 56) was represented by patients with MUO. The control group (n = 53) comprised children with metabolically healthy obesity (MHO). Serum levels of interleukin-1β (IL-1β) were measured using a chemiluminescent immunoassay (CLIA) method, interleukin-6, leptin, adiponectin – by enzyme-linked immunosorbent assay (ELISA) and the serum level of C-reactive protein were quantified by latex turbidimetric method (Synevo, Ukraine). The method of next-generation sequencing (NGS) (CeXGat, Germany) was used to identify LEPR SNP. Statistical methods were used: analysis of variance, Spearman’s correlation analysis and multiple discriminant analysis. Results. In obese children aged 6 to 18 years, there was an increase in pro-inflammatory adipokines IL-6 and leptin and a decrease in anti-inflammatory adiponectin. Statistically significant changes in these indicators were more expressed in the main group: IL-6 – 7.4 ± 0.5 pg/ml (ρ = 0.65; P ≤ 0.001); adiponectin – 3.9 ± 0.8 μg/ml (ρ = -0.27; P = 0.007) among all the children examined, leptin in girls – 47.8 ± 4.4 ng/ml (ρ = -0.28; P = 0.003) compared with the results of patients in the control group: IL-6 – 4.3 ± 0.3 pg/ml, adiponectin – 7.7 ± 2.4 μg/ml, leptin in girls – 32.5 ± 4.3 ng/ml, P ≤ 0.05. The most important in the development of MUO were the following SNP of the LEPR gene: rs3790435 (CiMUO = 0.939), rs2186248 (CiMUO = 0.862), P < 0.05. A strong correlation was found between MUO and serum IL-6 level (ρ = 0.7), LEPR SNP rs3790435 (ρ = 0.7), basal hyperinsulinemia (ρ = 0.72); Р ≤ 0.001. The risk of IL-6-dependent meta-inflammation in the presence of SNP rs3790435 of the LEPR gene: OR = 17.11; 95 % CI 2.8–20.4. Conclusions. Meta-inflammation in MUO is IL-6-dependent. Among the 10 SNPs of the LEPR gene that we identified, SNP rs3790435 of the LEPR gene has a strong association with the formation of MUO. SNP rs2186248 LEPR was described by us for the first time when it was found in 94.1 % of obese children, but it was characterized by the presence of a weak association with MUO.

Dissecting the contribution of single nucleotide polymorphisms in CCR9 and CCL25 genomic regions to the celiac disease phenotype

Purpose and objectivesGiven their role in homing immune cells to the intestine, CC motif chemokine receptor 9 (CCR9) and its specific ligand CC motif chemokine ligand 25 (CCL25) are interesting candidate genes for celiac disease. These genes are located in regions previously shown to be associated with or linked to celiac disease, but no investigations on their association with various celiac disease phenotypes have so far been conducted. Here we studied such associations of both genotyped and imputed single nucleotide polymorphisms (SNPs) with either regulatory function or exonic location of the CCR9 and CCL25 loci. ResultsExploiting a carefully phenotyped cohort of 625 celiac disease patients and 1817 non-celiac controls, we identified that multiple SNPs with predicted regulatory function (RegulomeDB score ≤3a and/or eQTL effect) located between 100 kB upstream and downstream of CCR9 and CCL25 are associated with celiac disease and/or selected phenotypes. Of the genotyped SNPs in the CCR9 loci, rs213360 with an eQTL effect on CCR9 expression in blood was associated with celiac disease and all investigated phenotypes except high HLA risk. Rs1545985 with an eQTL on CCR9 expression and rs7652331 and rs12493471, both with RegulomeDB score ≤3a, were all associated with gastrointestinal symptoms and malabsorption and the latter additionally with anemia. The genotyped CCL25 SNPs rs952444 and rs882951, with RegulomeDB scores 1d and 1f respectively and eQTL effect on CCL25 expression in small intestine, were associated with gastrointestinal symptoms and malabsorption. The CCL25 SNP rs2303165 identified in sequencing followed by imputation was associated with partial villous atrophy. However, the association did not pass the permutation based multiple testing correction (PEMP2 > 0.05). ConclusionsWe conclude that SNPs in the region of CCR9 and CCL25 with predicted functional effect or exonic localization likely contribute only modestly to various celiac disease phenotypes.

Analysis of association between FGB, MTHFR, MTR and MTRR genes polymorphisms and ischemic and hemorrhagic stroke

The genetic component is a leading factor of stroke manifestation. Contribution of single nucleotide polymorphisms or combined genotypes to disease development has population differences. Special attention should be paid to genetic features in different types of strokes among the Ukrainian population. The aim of the study was to estimate the association of polymorphisms between FGB, MTHFR, MTR, MTRR genes or gene-gene interaction and a risk of atherotrombotic ischemic stroke and intracranial hemorrhagic stroke among Ukrainians. Materials and methods. 102 patients with atherotrombotic ischemic stroke, 56 patients with intracranial hemorrhagic stroke and 102 healthy control subjects were included in the study. The control group comprised peoples without cardiovascular diseases, family history of stroke and with normal lipid profile values. The mean age was 53.4 ± 9.1 years for stroke patients and 54.5 ± 8.2 years for the control group. Single nucleotide polymorphisms С677T (rs1801133) MTHFR gene, A66G (rs1801394) MTRR gene, A2756G (rs 1805087) MTR gene, C-148T (rs 1800787) FGB gene were detected by polymerase chain reaction (PCR) followed by restriction of amplificated fragments and polymorphism A1298C (rs1801131) MTHFR gene was determined by allele specific PCR method. Results . The association between 1298СС genotype MTHFR gene (OR = 3.457, 95 % CI:1.053–11.357) and -148СТ genotype FGB gene (OR = 2.276, 95 % CI: 1.248–4.152) and a risk of atherotrombotic ischemic stroke was revealed. A risk of intracranial hemorrhagic stroke was associated with 66AG (OR = 2.643, 95 % CI: 1.059–6.593) and 66GG (OR = 4.826, 95 % CI: 1.858–12.535) genotypes of MTRR gene. Synergistic effect was shown for polymorphic loci of FGB/С-148Т and MTRR / A66G in atherotrombotic ischemic stroke development as well as independent effect of MTRR/A66G for intracranial hemorrhagic stroke. Conclusions. There are some differences in the genetic components of different types of acute stroke in Ukrainians that should be taken into account when initiating therapy or preventative measures.

Phenotypic and functional translation of IL1RL1 locus polymorphisms in lung tissue and asthmatic airway epithelium.

The IL1RL1 (ST2) gene locus is robustly associated with asthma; however, the contribution of single nucleotide polymorphisms (SNPs) in this locus to specific asthma subtypes and the functional mechanisms underlying these associations remain to be defined. We tested for association between IL1RL1 region SNPs and characteristics of asthma as defined by clinical and immunological measures and addressed functional effects of these genetic variants in lung tissue and airway epithelium. Utilizing 4 independent cohorts (Lifelines, Dutch Asthma GWAS [DAG], Genetics of Asthma Severity and Phenotypes [GASP], and Manchester Asthma and Allergy Study [MAAS]) and resequencing data, we identified 3 key signals associated with asthma features. Investigations in lung tissue and primary bronchial epithelial cells identified context-dependent relationships between the signals and IL1RL1 mRNA and soluble protein expression. This was also observed for asthma-associated IL1RL1 nonsynonymous coding TIR domain SNPs. Bronchial epithelial cell cultures from asthma patients, exposed to exacerbation-relevant stimulations, revealed modulatory effects for all 4 signals on IL1RL1 mRNA and/or protein expression, suggesting SNP-environment interactions. The IL1RL1 TIR signaling domain haplotype affected IL-33–driven NF-κB signaling, while not interfering with TLR signaling. In summary, we identify that IL1RL1 genetic signals potentially contribute to severe and eosinophilic phenotypes in asthma, as well as provide initial mechanistic insight, including genetic regulation of IL1RL1 isoform expression and receptor signaling.

Genetic variation of pentraxin-3 in Egyptian patients with chronic hepatitis C virus and hepatocellular carcinoma

Background Hepatocellular carcinoma (HCC) is one of the most common aggressive solid malignancies worldwide, particularly in Egypt. There is evidence of the contribution of single nucleotide polymorphisms (SNPs) in increasing cancer risk by influencing individual susceptibility to develop HCC. Pentraxin-3 (PTX3) has several functions in controlling cancer-related inflammation through regulation of the complement cascade, so acting as an extrinsic oncosuppressor gene. Several studies have discussed the association between PTX3 genetic polymorphism and cancer risk. Aim To study PTX3-(rs2305619)-SNP and the associated risk to develop HCC in patients with chronic hepatitis C virus (HCV), in addition to its possible correlation with HCV-RNA viral load and fibrosis degree in Egyptian patients with chronic HCV and HCC. Patients and methods A total of 40 patients with HCC on top of chronic HCV infection, 40 patients with chronic HCV, and 40 healthy participants were enrolled in the study. DNA was extracted from the peripheral blood, and PTX3-(rs2305619) genotyping was performed using real-time PCR. Results PTX3-(rs2305619) A/A polymorphic genotype was statistically significantly higher in both HCC and chronic HCV cases with advanced fibrosis than controls. The A/A genotype showed nine-fold increased risk of HCC when compared with healthy control (odds ratio=9.1, 95% confidence interval=2.304–35.94, P=0.002). A positive correlation was detected between A/A genotype and the higher HCV-RNA viral load in both HCV and HCC patients groups. Conclusion A allele of PTX3-(rs2305619) SNP could be considered as an independent molecular detector for HCC in Egyptian patients with chronic HCV.

Do Cerebral Small Vessel Disease and Multiple Sclerosis Share Common Mechanisms of White Matter Injury?

Background and Purpose- The role of inflammation in ischemic white matter disease is increasingly recognized, and further understanding of the pathophysiology might inform future treatment strategies. Multiple sclerosis (MS) is a chronic autoimmune condition in which inflammation plays a central role that also affects the white matter. We hypothesized that white matter injury might share common mechanisms and used statistical genetics techniques to assess whether having genetically elevated white matter hyperintensity (WMH) volume was associated with increased MS risk. Methods- We investigated the genetic association in 2 cohorts with magnetic resonance imaging-quantified ischemic white matter lesion volume (WMH in stroke; n=2797 and UK Biobank; n=8353) and 14 802 cases of MS and 26 703 controls from the International Multiple Sclerosis Genetics Consortium. We further performed individual-level polygenic risk score calculations for MS and measures of structural white matter disease in UK Biobank. Finally, we looked for evidence of overlapping risk across the whole genome. Results- There was no association of genetic variants influencing MS with WMH volume using summary statistics in the WMH in stroke cohort (relative risk score =1.014; 95% CI, 0.936-1.110) or in the UK Biobank cohort (relative risk score =1.030; 95% CI, 0.932-1.117). Conversely, assessing the contribution of single nucleotide polymorphisms significantly associated with WMH on the risk of MS there was no significant association (relative risk score =0.930; 95% CI, 0.736-1.191). There were no significant associations between polygenic risk scores calculations; these results were robust to the selection of single nucleotide polymorphisms at a range of significance thresholds. Whole genome analysis did not reveal any overlap of risk between the traits. Conclusions- Our results do not provide evidence to suggest a shared mechanism of white matter damage in ischemia and MS. We propose that inflammation acts in distinct pathways because of the differing nature of the primary insult.

Contribution of Gene Regulatory Networks to Heritability of Coronary Artery Disease

BackgroundGenetic variants currently known to affect coronary artery disease (CAD) risk explain less than one-quarter of disease heritability. The heritability contribution of gene regulatory networks (GRNs) in CAD, which are modulated by both genetic and environmental factors, is unknown. ObjectivesThis study sought to determine the heritability contributions of single nucleotide polymorphisms affecting gene expression (eSNPs) in GRNs causally linked to CAD. MethodsSeven vascular and metabolic tissues collected in 2 independent genetics-of-gene-expression studies of patients with CAD were used to identify eSNPs and to infer coexpression networks. To construct GRNs with causal relations to CAD, the prior information of eSNPs in the coexpression networks was used in a Bayesian algorithm. Narrow-sense CAD heritability conferred by the GRNs was calculated from individual-level genotype data from 9 European genome-wide association studies (GWAS) (13,612 cases, 13,758 control cases). ResultsThe authors identified and replicated 28 independent GRNs active in CAD. The genetic variation in these networks contributed to 10.0% of CAD heritability beyond the 22% attributable to risk loci identified by GWAS. GRNs in the atherosclerotic arterial wall (n = 7) and subcutaneous or visceral abdominal fat (n = 9) were most strongly implicated, jointly explaining 8.2% of CAD heritability. In all, these 28 GRNs (each contributing to >0.2% of CAD heritability) comprised 24 to 841 genes, whereof 1 to 28 genes had strong regulatory effects (key disease drivers) and harbored many relevant functions previously associated with CAD. The gene activity in these 28 GRNs also displayed strong associations with genetic and phenotypic cardiometabolic disease variations both in humans and mice, indicative of their pivotal roles as mediators of gene–environmental interactions in CAD. ConclusionsGRNs capture a major portion of genetic variance and contribute to heritability beyond that of genetic loci currently known to affect CAD risk. These networks provide a framework to identify novel risk genes/pathways and study molecular interactions within and across disease-relevant tissues leading to CAD.

Association of Single-Nucleotide Polymorphism REX1 rs6815391, OCT4 rs13409 or rs3130932, and CTBP2 rs3740535 with Primary Lung Cancer Susceptibility: A Case-Control Study in a Chinese Population

The purpose of the current study is to explore the contribution of single-nucleotide polymorphisms (SNPs) of REX1 rs6815391, OCT4 rs13409 or rs3130932, and CTBP2 rs3740535 to the risk of lung cancer. A questionnaire survey was used to obtain basic information of the included subjects. A case control study was performed in 1121 patients and 1121 controls. All subjects were subjected to blood sampling for genomic DNA extraction and genotyping of the cancer stem cell-associated gene SNPs, including REX1 rs6815391, OCT4 rs13409 or rs3130932, and CTBP2 rs3740535 by real-time PCR. The association with the risk of primary lung cancer and interaction with environmental factors were assessed using unconditional logistic regression for the odds ratios and corresponding 95% confidence intervals. The genotype frequency distribution of OCT4 rs13409 loci was statistically significant, but there was no significant difference in the rest of the loci between lung cancer patients and healthy controls. The OCT4 gene was also related with lung cancer susceptibility in the genetic model after adjusting for lung cancer-related factors. Despite the presence of the dominant or recessive model, the four loci polymorphisms were associated with pollution near the place of residence, house type, worse ventilation situation, smoking, passive smoking, cooking oil fumes (COF), and family history of cancer, which increased the risk of lung cancer. Nonmarried status, 18.5≤BMI, COF, smoking, passive smoking, family history of cancer, and history of lung disease were independent risk factors of lung cancer susceptibility. Additionally, college degree or above, no pollution near the place of residence, protective genotype 1 or 2, and well ventilation can reduce the occurrence of lung cancer. There is an interaction between the four loci and environmental factors, and OCT4 rs13409 is a risk factor of primary lung cancer.

Ficolins and the Recognition of Pathogenic Microorganisms: An Overview of the Innate Immune Response and Contribution of Single Nucleotide Polymorphisms.

Ficolins are innate pattern recognition receptors (PRR) and play integral roles within the innate immune response to numerous pathogens throughout the circulation, as well as within organs. Pathogens are primarily removed by direct opsonisation following the recognition of cell surface carbohydrates and other immunostimulatory molecules or via the activation of the lectin complement pathway, which results in the deposition of C3b and the recruitment of phagocytes. In recent years, there have been a number of studies implicating ficolins in the recognition and removal of numerous bacterial, viral, fungal, and parasitic pathogens. Moreover, there has been expanding evidence highlighting that mutations within these key immune proteins, or the possession of particular haplotypes, enhance susceptibility to colonization by pathogens and dysfunctional immune responses. This review will therefore encompass previous knowledge on the role of ficolins in the recognition of bacterial and viral pathogens, while acknowledging the recent advances in the immune response to fungal and parasitic infections. Additionally, we will explore the various genetic susceptibility factors that predispose individuals to infection.

Risk Factor Genes in Patients with Dystonia: A Comprehensive Review.

BackgroundDystonia is a movement disorder with high heterogeneity regarding phenotypic appearance and etiology that occurs in both sporadic and familial forms. The etiology of the disease remains unknown. However, there is increasing evidence suggesting that a small number of gene alterations may lead to dystonia. Although pathogenic variants to the familial type of dystonia have been extensively reviewed and discussed, relatively little is known about the contribution of single-nucleotide polymorphisms (SNPs) to dystonia. This review focuses on the potential role of SNPs and other variants in dystonia susceptibility.MethodsWe searched the PubMed database for peer-reviewed articles published in English, from its inception through January 2018, that concerned human studies of dystonia and genetic variants. The following search terms were included: “dystonia” in combination with the following terms: 1) “polymorphisms” and 2) “SNPs” as free words.ResultsA total of 43 published studies regarding TOR1A, BDNF, DRD5, APOE, ARSG, NALC, OR4X2, COL4A1, TH, DDC, DBH, MAO, COMT, DAT, GCH1, PRKRA, MR-1, SGCE, ATP1A3, TAF1, THAP1, GNAL, DRD2, HLA-DRB, CBS, MTHFR, and MS genes, were included in the current review.DiscussionTo date, a few variants, which are possibly involved in several molecular pathways, have been related to dystonia. Large cohort studies are needed to determine robust associations between variants and dystonia with adjustment for other potential cofounders, in order to elucidate the pathogenic mechanisms of dystonia and the net effect of the genes.

PPAR and GST polymorphisms may predict changes in intellectual functioning in medulloblastoma survivors.

Advances in the treatment of pediatric medulloblastoma have led to improved survival rates, though treatment-related toxicity leaves children with significant long-term deficits. There is significant variability in the cognitive outcome of medulloblastoma survivors, and it has been suggested that this variability may be attributable to genetic factors. The aim of this study was to explore the contributions of single nucleotide polymorphisms (SNPs) in two genes, peroxisome proliferator activated receptor (PPAR) and glutathione-S-transferase (GST), to changes in general intellectual functioning in medulloblastoma survivors. Patients (n = 44, meanage = 6.71years, 61.3% males) were selected on the basis of available tissue samples and neurocognitive measures. Patients received surgical tumor resection, craniospinal radiation, radiation boost to the tumor site, and multiagent chemotherapy. Genotyping analyses were completed using the Illumina Human Omni2.5 BeadChip, and 41 single nucleotide polymorphisms (SNPs) were assessed across both genes. We used a machine learning algorithm to identify polymorphisms that were significantly associated with declines in general intellectual functioning following treatment for medulloblastoma. We identified age at diagnosis, radiation therapy, chemotherapy, and eight SNPs associated with PPARs as predictors of general intellectual functioning. Of the eight SNPs identified, PPARα (rs6008197), PPARγ (rs13306747), and PPARδ (rs3734254) were most significantly associated with long-term changes in general intellectual functioning in medulloblastoma survivors. PPAR polymorphisms may predict intellectual outcome changes in children treated for medulloblastoma. Importantly, emerging evidence suggests that PPAR agonists may provide an opportunity to minimize the effects of treatment-related cognitive sequelae in these children.

Contribution of single-nucleotide polymorphism in transcription factor 7-like 2 gene to cardiometabolic risk in adult Nigerians

Background: Single-nucleotide polymorphism in the gene, transcription factor 7-like 2 (TCF7L2), shows the strongest and most consistent association with risk of developing type 2 diabetes (T2D). TCF7L2 has been associated with both impaired beta-cell function and insulin resistance. Gene variants of TCF7L2 may, therefore, contribute to cardiometabolic risk (CMR) and metabolic syndrome (MS). Aims and Objectives: The study aims to examine the relationship between gene variants in TCF7L2 with MS and CMR. Methods: Three hundred and fifty-six adult Nigerians aged between 40 and 100 years participated in a cross-sectional, analytical study. The association between TCF7L2 genotypes and MS and its components was determined. The data were analyzed, and statistical significance was set at P Results: Three hundred and fifty-six individuals participated in the study (35.6% of males and 64.2% of females). About 64.9% of participants had T2D. The prevalence of MS was 26.4%. Among the individuals with the wild-type homozygote genotype CC, heterozygote genotype CT, and homozygote mutant TT, 24.9%, 27.2%, and 30.6% had MS, respectively. The risk T allele was associated with higher mean values of waist circumference and triglyceride than the C allele (P = 0.006 and 0.022, respectively). The T allele had a significant correlation with MS components (P Conclusion: Variants in the TCF7L2 gene are associated with components of MS and correlate with CMR through insulin resistance.