Functional Gene Polymorphisms Research Articles

Conceptualization of functional single nucleotide polymorphisms of polycystic ovarian syndrome genes: an in silico approach

PurposePolycystic ovarian syndrome (PCOS) is a multi-faceted endocrinopathy frequently observed in reproductive-aged females, causing infertility. Cumulative evidence revealed that genetic and epigenetic variations, along with environmental factors, were linked with PCOS. Deciphering the molecular pathways of PCOS is quite complicated due to the availability of limited molecular information. Hence, to explore the influence of genetic variations in PCOS, we mapped the GWAS genes and performed a computational analysis to identify the SNPs and their impact on the coding and non-coding sequences. MethodsThe causative genes of PCOS were searched using the GWAS catalog, and pathway analysis was performed using ClueGO. SNPs were extracted using an Ensembl genome browser, and missense variants were shortlisted. Further, the native and mutant forms of the deleterious SNPs were modeled using I-TASSER, Swiss-PdbViewer, and PyMOL. MirSNP, PolymiRTS, miRNASNP3, and SNP2TFBS, SNPInspector databases were used to find SNPs in the miRNA binding site and transcription factor binding site (TFBS), respectively. EnhancerDB and HaploReg were used to characterize enhancer SNPs. Linkage Disequilibrium (LD) analysis was performed using LDlink.Results25 PCOS genes showed interaction with 18 pathways. 7 SNPs were predicted to be deleterious using different pathogenicity predictions. 4 SNPs were found in the miRNA target site, TFBS, and enhancer sites and were in LD with reported PCOS GWAS SNPs.ConclusionComputational analysis of SNPs residing in PCOS genes may provide insight into complex molecular interactions among genes involved in PCOS pathophysiology. It may also aid in determining the causal variants and consequently contributing to predicting disease strategies.

SIRT1 functional polymorphisms (rs12778366, rs3758391) as genetic biomarkers of susceptibility to type 2 diabetes mellitus in Iranians: a case-control study and computational analysis

Genetic background is an important risk factor for type 2 diabetes mellitus (T2DM). We designed this study to examine the role of rs12778366 and rs3758391, two functional SIRT1 gene polymorphisms, on the risk of T2DM in an Iranian population. In this case-control study, a total of 813 subjects were enrolled. SNPs were genotyped via polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Multiple computational analyses were also performed to examine the potential effects of the studied variants. We found a significant association between rs12778366 polymorphism and an enhanced risk of T2DM under allelic C vs. T (OR = 1.50), codominant TC vs.TT (OR = 1.86), dominant CC + TC vs. TT (OR = 1.65), and over-dominant TC vs. CC + TT (OR = 1.80) genetic models. In contrast, codominant CT vs. CC (OR = 0.54) and dominant CT + TT vs. CC (OR = 0.68) models of rs3758391 polymorphism were correlated with decreased risk of T2DM. Compared to the TC haplotype, we have found that the CC combination significantly enhanced the risk of T2DM by 1.86-fold. Computational analyses indicated that the C allele of rs12778366 might disrupt the binding site of the CEBP transcription factor. SIRT1 rs12778366 and rs3758391 polymorphisms might be associated with T2DM susceptibility in our population. Replications in different races with larger sample sizes are necessary to yield more accurate results.

Genetic variants in NKG2D axis and susceptibility to Epstein-Barr virus-induced nasopharyngeal carcinoma.

Nasopharyngeal carcinoma (NPC) is a rare epithelial carcinoma arising from the nasopharyngeal region. The pathogenesis of NPC is linked to Epstein-Barr virus (EBV) infection, although genetics and lifestyle factors appears to be also implicated. NKG2D is an immunoreceptor expressed by NK and T-cell subsets that recognizes MICA protein and other ligands on tumor cells. NKG2D interaction with MICA plays a role in the immunosurveillance to viruses and cancer. We investigated potential associations between functional polymorphisms in NKG2D and MICA genes with NPC susceptibility. We conducted a case-control study including 255 Vietnamese patients with EBV + non-differentiated NPC and 220 healthy controls. We observed a significant association between the LNK/LNK genotype of rs1049174 (a variant associated with lower NKG2D receptor expression and reduced NK cell cytotoxicity) and increased susceptibility to NPC (adjusted OR = 1.66, 95% CI 1.07-2.59; p = 0.024). Similarly, the AA genotype of MICA rs2596542 was significantly associated with NPC (adjusted OR = 2.12; 95% CI 1.22-3.81; p = 0.009). In addition, tumor specimens of NPC patients with the AA genotype displayed a higher expression level of MICA proteins and showed higher EBV titers compared with tumor tissues from patients with the GG or GA genotypes. Higher EBV copy numbers were also observed in tumors with the A allele of MICA rs1051792 (also known as MICA-129 Met/Val) compared with those with the G allele; however, MICA rs1051792 variants were not associated with NPC susceptibility. These results suggest that genetic variants in components of the NKG2D axis may influence the individual susceptibility to EBV-induced NPC.

Pharmacogenetics of advanced lung cancer: Predictive value of functional genetic polymorphism AGXT Pro11Leu in clinical outcome?

IntroductionAGXT gene codes for the enzyme alanine glyoxylate aminotransferase, which is involved in hepatic peroxisomal metabolism of platinum-based chemotherapeutic agents. The association of genetic variant AGXT rs34116584 on the clinical outcome and response to chemotherapy of patients with non-small cell lung cancer (NSCLC) remains to be established. Our aim was to evaluate the association of functional AGXT gene polymorphism in NSCLC progression, considering as primary and secondary endpoint, progression free survival (PFS) and overall survival (OS), respectively. MethodsGenotyping of theAGXT rs34116584 genetic polymorphism was performed by mass spectrometry on 168 DNA samples from patients with NSCLC (stages IIIA-IVB). Univariate survival analysis included the study of Kaplan-Meier curves with the Log-Rank test, while Cox regression was used as a multivariate analysis. ResultsMultivariate analysis showed shorter PFS for T carriers [HR=2.0, 95% CI, 1.4−3.0, p<0.0001] and shorter OS [HR=1.8, 95% CI, 1.1−3.0, p=0.017] globally, as well as in a subgroup of patients (n=144) treated with first line platinum-based chemotherapy [HR=2.0, 95% CI, 1.3–3.1, p=0.001] and [HR=1.8, 95% CI, 1.1–3.1, p=0.026], respectively. ConclusionThis polymorphism seems to have an impact on NSCLC progression, opening new perspectives for its inclusion as a pharmacogenetic predictor of response to platinum-based chemotherapy.

The Angiotensin-converting Enzyme Insertion/Deletion Polymorphism as a Common Risk Factor for Major Pregnancy Complications.

Idiopathic pregnancy complications pose a major threat to both maternal and fetal health worldwide. Numerous studies have implicated the role of the renin-angiotensin system (RAS) in the development of obstetric syndromes, since it is crucial for the uteroplacental function. A major RAS component is the angiotensin-converting enzyme (ACE), which hydrolyses angiotensin I to angiotensin II, and not only regulates arterial pressure, but also fibrinolytic activity, indirectly, through the expression of plasminogen activator inhibitor-1. A key functional polymorphism of the ACE gene is the insertion/deletion (I/D) polymorphism, which affects gene expression and product levels, and can therefore lead to high blood pressure and/or reduced fibrinolytic activity. These can cause major pregnancy complications, such as preeclampsia, recurrent pregnancy loss and preterm birth. This review discusses how the ACE I/D is associated with susceptibility towards pregnancy complications, on its own or in combination with other functional gene polymorphisms such, as the angiotensin II receptor type 1 (AT1R) A1166CC, angiotensin II receptor type 2 (AT2R) G1332A, plasminogen activator inhibitor-1 (PAI-1) 4G/5G, matrix metallopeptidase-9 (MMP-9) C1562T, angiotensinogen (AGT) M235T, renin (REN) 83A/G, factor XIII (F13) Val34Leu and endothelial nitric oxide synthase (eNOS) 4a/b.

Cytokine gene functional polymorphisms and phenotypic expression as predictors of evolution from latent to clinical rheumatic heart disease

IntroductionInflammation associated with rheumatic heart disease (RHD) is influenced by gene polymorphisms and inflammatory cytokines. There are currently no immunologic and genetic markers to discriminate latent versus clinical patients, critical to predict disease evolution. Employing machine-learning, we searched for predictors that could discriminate latent versus clinical RHD, and eventually identify latent patients that may progress to clinical disease. MethodsA total of 212 individuals were included, 77 with latent, 100 with clinical RHD, and 35 healthy controls. Circulating levels of 27 soluble factors were evaluated using Bio-Plex ProTM® Human Cytokine Standard 27-plex assay. Gene polymorphism analyses were performed using RT-PCR for the following genes: IL2, IL4, IL6, IL10, IL17A, TNF and IL23. ResultsSerum levels of all cytokines were higher in clinical as compared to latent RHD patients, and in those groups than in controls. IL-4, IL-8, IL-1RA, IL-9, CCL5 and PDGF emerged in the final multivariate model as predictive factors for clinical, compared with latent RHD. IL-4, IL-8 and IL1RA had the greater power to predict clinical RHD. In univariate analysis, polymorphisms in IL2 and IL4 were associated with clinical RHD and in the logistic analysis, IL6 (GG + CG), IL10 (CT + TT), IL2 (CA + AA) and IL4 (CC) genotypes were associated with RHD. ConclusionDespite higher levels of all cytokines in clinical RHD patients, IL-4, IL-8 and IL-1RA were the best predictors of clinical disease. An association of polymorphisms in IL2, IL4, IL6 and IL10 genes and clinical RHD was observed. Gene polymorphism and phenotypic expression of IL-4 accurately discriminate latent versus clinical RHD, potentially instructing clinical management.

Germline Genetic Variants of the Renin-Angiotensin System, Hypoxia and Angiogenesis in Non-Small Cell Lung Cancer Progression: Discovery and Validation Studies.

Simple SummaryThe presence of polymorphic gene variants in the human genome provides extensive genetic (and eventually phenotypic) variation affecting both normal physiological mechanisms and cancer pathogenesis. Functional genetic polymorphisms might have predictive and/or prognostic value in lung cancer, opening novel opportunities to improve prediction and guide clinical reasoning and therapeutics in lung cancer patients. Recent knowledge pinpoints a pleiotropic role for renin-angiotensin system, particularly in the lung and mainly through locally regulated alternative molecules and secondary pathways. Dysregulation of this system play a role in cell proliferation, hypoxia and angiogenesis, which processes are involved in lung cancer progression. Here we suggest that polymorphic variants in genes coding for renin-angiotensin system might play a role in Non-Small Cell Lung Cancer progression.Introduction: The renin–angiotensin system (RAS) is involved in cell proliferation, immunoinflammatory response, hypoxia and angiogenesis, which are critical biological processes in lung cancer. Our aim was to study the association of putatively functional genetic polymorphisms in genes coding for proteins involved in RAS, hypoxia and angiogenesis with non-small cell lung cancer (NSCLC) prognosis. Methods: Genotyping of 52 germline variants from genes of the RAS and hypoxic/angiogenic factors/receptors was performed using MassARRAY iPLEX Gold in a retrospective cohort (n = 167) of advanced NSCLC patients. Validation of the resulting genetic markers was conducted in an independent group (n = 190), matched by clinicopathological characteristics. Results: Multivariate analysis on the discovery set revealed that MME rs701109 C carriers were protected from disease progression in comparison with homozygous T (hazard ratio (HR) = 0.5, 95% confidence interval (CI) = 0.2–0.8, p = 0.010). Homozygous A and T genotypes for KDR rs1870377 were at increased risk for disease progression and death compared to heterozygous (HR = 1.7, 95% CI = 1.2–2.5, p = 0.005 and HR = 2.1, 95% CI = 1.2–3.4, p = 0.006, respectively). Carriers of homozygous genotypes for ACE2 rs908004 presented increased risk for disease progression, only in the subgroup of patients without tumour actionable driver mutations (HR = 2.9, 95% CI = 1.3–6.3, p = 0.010). Importantly, the association of homozygous genotypes in MME rs701109 with risk for disease progression was confirmed after multivariate analysis in the validation set. Conclusion: This study provides evidence that MME polymorphism, which encodes neprilysin, may modulate progression-free survival in advanced NSCLC. Present genetic variation findings will foster basic, translational, and clinical research on their role in NSCLC.

Association of dopamine transporter gene polymorphisms with the risk of Parkinson's Disease

Introduction: Parkinson's disease (PD) is a second most common neurodegenerative disease. Age, genetic and environmental factors play important role in PD pathogenesis. Current study is aimed to identify the functional dopamine transporter gene polymorphisms - SLC6A3, SLC6A4, and SLc18A2 involved in PD pathogenesis in south Indian population.

Predisposition to Hyperthyroidism May Be Influenced by Functional TNF-α, IL-1, IL-6, and IL-10 Polymorphisms: A Meta-Analysis

Background: Predisposition to hyperthyroidism may be influenced by functional gene polymorphisms in tumor necrosis factor-α (TNF-α), interleukin-1 (IL-1), interleukin-4 (IL-4), interleukin-6 (IL-6), and interleukin-10 (IL-10). However, the results of the studies published so far remain discrepant, so we conducted a meta-analysis to more robustly investigate relationships between TNF-α/IL-1/IL-4/IL-6/IL-10 polymorphisms and predisposition to hyperthyroidism. Methods: A comprehensive literature retrieval from PubMed, Embase, Web of Science, WanFang, VIP, and CNKI was endorsed by the authors, and 38 studies were found to be eligible for pooled meta-analyses. Results: We found that genotypic frequencies of TNF-α −308 G/A, IL-1A −889 C/T, IL-6 −174 G/C, IL-6 −572 G/C, IL-10 −819 C/T, and IL-10 −1082 A/G polymorphisms among cases were significantly different from those among controls. Moreover, we also found that genotypic frequencies of TNF-α −308 G/A and IL-6 −174 G/C polymorphisms among cases of Caucasian origin were significantly different from those among Caucasian controls, and genotypic frequencies of IL-1A −889 C/T, IL-1B −511 C/T, IL-6 −174 G/C, IL-6 −572 G/C, and IL-10 −1,082 A/G polymorphisms among cases of Asian origin were also significantly different from those among Asian controls. Conclusions: This meta-analysis suggests that TNF-α −308 G/A, IL-1A −889 C/T, IL-1B −511 C/T, IL-6 −174 G/C, IL-6 −572 G/C, IL-10 −819 C/T, and IL-10 −1,082 A/G polymorphisms may influence predisposition to hyperthyroidism in certain ethnic groups.

Exposure to household air pollution over 10 years is related to asthma and lung function decline

We investigated if long-term household air pollution (HAP) is associated with asthma and lung function decline in middle-aged adults, and whether these associations were modified by glutathione S-transferase (GST) gene variants, ventilation and atopy. Prospective data on HAP (heating, cooking, mould and smoking) and asthma were collected in the Tasmanian Longitudinal Health Study (TAHS) at mean ages 43 and 53 years (n=3314). Subsamples had data on lung function (n=897) and GST gene polymorphisms (n=928). Latent class analysis was used to characterise longitudinal patterns of exposure. Regression models assessed associations and interactions. We identified seven longitudinal HAP profiles. Of these, three were associated with persistent asthma, greater lung function decline and % reversibility by age 53 years compared with the "Least exposed" reference profile for those who used reverse-cycle air conditioning, electric cooking and no smoking. The "All gas" (OR 2.64, 95% CI 1.22-5.70), "Wood heating/smoking" (OR 2.71, 95% CI 1.21-6.05) and "Wood heating/gas cooking" (OR 2.60, 95% CI 1.11-6.11) profiles were associated with persistent asthma, as well as greater lung function decline and % reversibility. Participants with the GSTP1 Ile/Ile genotype were at a higher risk of asthma or greater lung function decline when exposed compared with other genotypes. Exhaust fan use and opening windows frequently may reduce the adverse effects of HAP produced by combustion heating and cooking on current asthma, presumably through increasing ventilation. Exposures to wood heating, gas cooking and heating, and tobacco smoke over 10 years increased the risks of persistent asthma, lung function decline and % reversibility, with evidence of interaction by GST genes and ventilation.

Роль полиморфных маркеров гена IL10 в патогенезе сахарного диабета 1-го типа

Сахарный диабет типа 1 (СД1) представляет собой многофакторное заболевание, которое характеризуется аутоиммунной природой. Важным фактором в патогенезе СД1 является генетическая предрасположенность, характеризующаяся наличием функциональных однонуклеотидных замен (SNP) в генах цитокинов, ответственных за воспаление. Предполагают, что длительное хроническое воспаление приводит к необратимому разрушению β-клеток поджелудочной железы и может быть объяснено наличием функциональных полиморфных маркеров в генах-антагонистах. Цель исследования - изучение частоты аллельных вариантов ряда полиморфных маркеров гена IL10 при СД1 у жителей Москвы и Московской области. Методика. В работу включено 366 больных СД 1 типа и 526 здоровых индивидов русского происхождения. Группу больных составили пациенты с наличием сахарного диабета 1 типа различной манифестации с общей медианой 41±5 лет. Обе группы выравнены по полу и возрасту. Определение генотипов полиморфных маркеров rs1800896, rs1800872 и rs3024505 гена IL10 проводилось с помощью ПЦР «в реальном времени» на амплификаторе «Real-time CFX96 Touch» (Bio-Rad, США) с использованием готовой смеси для ПЦР qPCRmix-HS (Евроген, Россия) и уникальных праймеров и зондов. Результаты. В результате проведенного исследования выявлена статистически значимая ассоциация полиморфного маркера rs1800896 гена IL10 с повышенным риском развития СД1 (χ2=15.52, OR=1.48, CI95%=1.23-1.79, р=0,0004). Заключение. Полученные результаты дополняют информацию о механизмах возникновения СД типа 1. Внедрение в практику анализа полиморфных вариантов гена IL10 позволит выявить предрасположенность к развитию этого заболевания, его прогрессированию у пациентов с аутоиммунными заболеваниями и у лиц, находящихся в группе риска. Type 1 diabetes mellitus (T1DM) is a multifactorial disease of an autoimmune origin. An important factor in the pathogenesis of T1DM is genetic predisposition characterized by the presence of functional single-nucleotide polymorphisms (SNPs) in the cytokine genes contributing to inflammation. Long-standing, chronic inflammation is considered to result in irreversible destruction of all pancreatic b-cells and may be due to the presence of functional polymorphic markers in genes of inflammation antagonists, such as the interleukin 10 (IL10) gene. Aim. The aim of this study was to determine the frequency of allelic variants in a number of IL10 gene polymorphic markers in residents of Moscow and the Moscow Region with T1DM. Methods. The study includes 366 patients with T1DM with different manifestations and a median duration of 41+5 years and 526 healthy individuals. The groups were gender- and age-matched. Genotypes of the rs1800896, rs1800872, and rs3024505 polymorphic markers of the IL10 gene were determined with real-time PCR on a Real-Time CFX96 Touch amplifier (Bio-Rad, USA) with a qPCRmix-HS ready-mixed PCR kit (Eurogen, Russia) and unique primers and probes. Results. The rs1800896 polymorphic marker of the IL10 gene statistically significantly correlated with increased risk of T1DM (χ2=15.52, OR=1.48, CI95%=1.23-1.79, р=0.0004). Conclusion. The study results complement the information about T1DM mechanisms of origin and pathogenesis. Implementation in practice of the methods for analyzing polymorphic variants of the IL10 gene will allow revealing a predisposition to this disease and/or its progression in patients with autoimmune diseases or in people at risk.

Contribution of Five Functional Loci of Dopamine Metabolism-Related Genes to Parkinson’s Disease and Multiple System Atrophy in a Chinese Population

Background: Impaired dopamine metabolism is associated with Parkinson’s disease (PD). Considering the overlap in the clinical and pathological characteristics between PD and multiple system atrophy (MSA), we investigated the effect of five potential functional polymorphisms in dopamine metabolism-related genes on disease susceptibility, phenotypes, and responses to dopamine in a large sample of PD and MSA patients.Methods: A total of 1506 PD patients, 496 MSA patients, and 894 healthy controls were included in this study. Five variants (rs6356 in TH, rs921451 in DDC, rs4680 in COMT, rs1799836 in MAOB, and rs1611115 in DBH) were genotyped in all cases using Sequenom iPLEX Assay technology.Results: After adjusting for gender and age at onset, except for DDC rs921451, which was associated with an increased risk of MSA (p = 0.001, OR = 1.21), no significant differences were found in genotype distribution or minor allele frequencies for the other four variants between PD and MSA patients and healthy controls. In the subgroup analysis, DDC rs921451 was associated with an increased risk for late-onset PD as well as for PD onset in males (p = 0.002 [OR = 1.13] p = 0.003 [OR = 1.15], respectively). In addition, patients harboring the risk allele DDC rs921451 required lower levodopa equivalent daily doses of dopaminergic medication than those without the risk allele (52.00 ± 21.31 mg/day, p = 0.015).Conclusion: None of the five candidate functional variants is a major determinant of the risk for PD or MSA. The modified PD phenotypes associated with these variants requires further confirmation.

The Polymorphism rs2968 of LSS Gene Confers Susceptibility to Age-Related Cataract

Research showed that lanosterol can decrease protein aggregation in lens and reduce cataract formation. Lanosterol synthase (LSS) and 3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR) are the limiting enzymes in the process of synthesis of lanosterol. We demonstrate to investigate the association between functional single-nucleotide polymorphisms (SNPs) of LSS and HMGCR genes and age-related cataract (ARC) risks in Han Chinese population from Jiangsu Eye Study. This is a case-control study. We collected participants' venous blood for DNA genotyping and lens capsule samples for RNA. The SNPs of the genes were assayed with TaqMan RT-PCR genotyping. The quantitative RT-PCR was used to detect the LSS mRNA levels of lens epithelial cells (LECs) in individuals. The chi-square test was used to compare differences between ARC groups and controls of each SNP and to calculate the odds ratio (OR). We found that LSS-rs2968 of ARCs was different from controls (p = 0.018), but the significance was lost after Bonferroni correction (p = 0.072). We then further performed stratification analysis and found that LSS-rs2968 A allele was associated with nuclear type of ARC risk in Chinese population (p = 0.012, OR = 0.68). Consequently, we found that the mRNA expression of LSS was lower in LECs of all subtypes of ARC group than that of control group (p < 0.05). LSS-rs2968 A allele might play a role in the formation and development of nuclear type of ARC risk in Chinese population.

Impact of Matrix Metalloproteinases 2 and 9 and Tissue Inhibitor of Metalloproteinase 2 Gene Polymorphisms on Allograft Rejection in Pediatric Renal Transplant Recipients.

Acute and chronic allograft rejection have been continuously an important obstacle in the follow-up of renal transplant recipients. During clinical management, several factors acting simultaneously result in acute rejection and chronic allograft nephropathy. Matrix metalloproteinases and tissue inhibitors of metalloproteinases are responsible for the organization of the extracellular matrix and play roles in cell proliferation and cellular invasion. Changes in matrix metalloproteinase expression levels have been reported to be associated with renal allograft rejection and interstitial fibrosis. In this study, we aimed to investigate functional polymorphisms of MMP2, MMP9, and TIMP2 genes in pediatric renal transplant recipients. Our study included 68 kidney transplant recipients and 58 control patients. The kidney transplant recipient group was further divided into 2 subgroups: no graft rejection (n = 47) and graft rejection (n =21). MMP2 -735C >T (rs2285053), MMP2 -1306C >T (rs243865), MMP2 -1575G >A (rs243866), MMP9 c.-1562C >T (rs3918242), TIMP2 -418G >C (rs8179090), and TIMP2 303C > T (rs2277698) polymorphisms were analyzed with the use of polymerase chain reaction and restriction fragment-length polymorphism methods. Allele prevalence was compared with reference values of the control group, and Hardy-Weinberg equilibrium was tested. Mean ages were 16.7 ± 3.9 years for the study group and 14.8 ± 5.6 years for the control group. The mean follow-up time after transplant was 37.7 ± 7.9 months. We compared allele frequencies in the 2 groups and calculated a statistically significant difference in rs2285053, rs243865, rs243866, rs3918242, rs8179090, and rs2277698 polymorphism frequencies between the transplant recipients and control patients. When the transplant recipient group was compared in itself with regard to allograft rejection, all investigated polymorphisms except TIMP2 -418G >C (rs8179090) revealed a statistically significant difference between those with and without rejection (P < .05). Matrix metalloproteinases and their tissue inhibitors could be important predictive biological markers for the follow-up of kidney transplant recipients.

C3 Gene Functional Polymorphisms and C3 Serum Levels in Patients with Rheumatoid Arthritis

ABSTRACT The complement system is a key component of the innate immunity that plays a significant role in the development and clinical presentation of Rheumatoid arthritis (RA). Complement protein C3 is a central molecule in the activation of complement with a significant role in the inflammatory processes of RA. Nevertheless, the impact of C3 gene polymorphisms in the development of RA is still unknown. The current study aimed to investigate the possible influence of C3 gene polymorphisms in the susceptibility and clinical expression of RA. Three C3 polymorphisms (rs2250656:A > G, intron 2; rs2230199:C > G [p.Arg102Gly], exon 3 and rs1047286:C > T [p.Pro314Leu], exon 9) were assessed by sequence-specific PCR in a total of 156 RA patients and 270 healthy controls from Southern Brazil. In addition, C3 levels were measured in 60 patients and 60 controls by immunoturbidimetry and clinical features were collected from medical records. The frequency of rs2230199 G allele and GG genotype was significantly higher in RA patients than controls (padj = 0.012 OR = 1.57 [1.11–2.31]; padj = 0.008, OR = 1.60 [1.35–2.33]) as well as the rs1047286 T and TT (padj = 0.010, OR = 1.67 [1.12–2.40]; padj = 0.001, OR = 1.83 [1.27–2.65] and the C3 AGT haplotype (padj = 0.0007 OR = 1.92 [1.32–2.80]). Moreover, C3 serum levels were higher in patients than controls (median: 169 mg/dl vs.155 mg/dl; padj = 0.022), as well as in RF seronegative compared with seropositive patients (172 mg/dl vs. 165 mg/dl; padj = 0.007). Our results suggest that the rs2230199 G (p.102Gly) and rs1047286 T (p.314Leu) alleles play a role in the pathophysiology of RA, possibly impacting complement activation by the alternative pathway.

Functional miR29a gene polymorphism enhanced the risk of chronic kidney disease in an Iranian population: A preliminary case-control study and bioinformatics analyses

BackgroundChronic kidney disease (CKD) is a global challenge that clusters within families. MicroRNAs have been introduced as candidate markers in predisposition to CKD, but the underlying mechanism has remained mostly unknown. The current preliminary study was designed to examine the effects of rs157907A/G, a functional variant located in the miR29a gene, on the risk of CKD in a population of Iranian ancestry. MethodsThree hundred forty unrelated Iranian subjects were enrolled between June 2019 and February 2020. Genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP)method. Bioinformatics tools were utilized to determine the potential effects of the variant. ResultsOur finding demonstrated that the presence of the G allele of rs157907A/G increased the risk of CKD by 1.50 fold. Also, enhanced risk of CKD was observed under codominant AG (OR = 1.86 95%CI = 1.16–2.96, p = 0.01), codominant GG (OR = 2.82 95%CI = 1.11–7.14, p = 0.02), dominant AG + GG vs. AA (OR = 1.93 95%CI = 1.22–3.06, p = 0.01) and overdominant AG + GG vs. AG (OR = 1.57 95%CI = 1.01–2.43, p = 0.04) contrasted genetic models. However, no significant association was noticed between genotypes and CKD stages (p = 0.59). Results of bioinformatics analysis indicated that miR29a structure is more stable in the presence of the G allele compared to A allele in the position of the variation. ConclusionThe findings of our study highlight the possible impact of a functionalmiR-29avariant in the pathophysiology of CKD. Identifying such SNPs will pave the way for the diagnosis and treatment of CKD, especially in advance stages.

The Influence of Endothelial Nitric Oxide Synthase (eNOS) Genetic Polymorphisms on Cholesterol Blood Levels Among Type 2 Diabetic Patients on Atorvastatin Therapy.

Endothelial nitric oxide synthase (eNOS) plays a major role in the response of anti-hypercholesterol statin drugs. Genetic polymorphisms in the eNOS gene affect the activity of eNOS thereby modulating the statin response. This study investigated the influence of major functional eNOS gene polymorphisms (rs2070744, rs1799983, and rs61722009) on the lipid profile of type 2 diabetes mellitus (T2DM) Jordanian patients treated with atorvastatin. The sample comprised 103 T2DM patients who attended the diabetes clinic of Jordan University Hospital. The T2DM patients had regularly been taking 20 mg atorvastatin. The atorvastatin response was calculated by measuring the lipid profile before and after three months of atorvastatin treatment. The eNOS genotypes of the subjects were analyzed using polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP) assay. No significant association was found between eNOS genetic polymorphisms and the response to atorvastatin (ANOVA, p > 0.05). In addition, no significant difference in the frequency of eNOS genotypes was found between T2DM patients and healthy subjects. However, patients with eNOS rs1799983, 4a/4a, and rs61722009 G/G genotypes showed significantly lower levels of baseline total cholesterol (TC) and low density lipoprotein (LDL) than did patients carrying the rs1799983 4b/4b or rs61722009 T/T genotype (p < 0.05). The eNOS rs1799983 and rs61722009 polymorphisms were in complete linkage disequilibrium (D' = 1). Although no association was found between eNOS genetic polymorphisms and atorvastatin response, there was a significant association between the rs1799983 and rs61722009 genotypes and baselines levels of TC and LDL in Jordanian T2DM patients. These genetic variants affect cholesterol levels and may play a role in the susceptibility to cardiovascular diseases in T2DM patients. Further studies are needed to validate these findings.

Association study of common functional genetic polymorphisms in SLC6A4 (5-HTT) and MAOA genes with obesity in portuguese children

Objectives To investigate the association of polymorphisms in SLC6A4 and MAOA genes with obesity indices in children. Material and Methods A total of 637 Portuguese children (317 girls; 320 boys) aged 3–11 years-old were genotyped for the SLC6A4 polymorphisms, 5-HTTLPR and STin2, and for a MAOA VNTR. Polymorphisms were analysed by PCR-based methods. Results Although non-significant (p = .089), our study revealed the Stin2 10 minor allele with a marked higher frequency in girls with overweight/obesity (0.466) in comparison with controls (0.376). Combining the two SLC6A4 polymorphisms, haplotype S/12 revealed in girls significant or nominally significant protective effects against BMI (β = −0.615; p = .009), BMI Z-score (β = −0.251; p = .006), WC (β = −1.4; p = .02) and WHtR (β = −0.008; p = .04). Conclusions We found some evidences for the role of SLC6A4 gene in measures of childhood obesity, mainly in girls.

Functional polymorphisms of BCL11A and HBS1L-MYB genes affect both fetal hemoglobin level and clinical outcomes in a cohort of children with sickle cell anemia.

Fetal hemoglobin (HbF) ameliorates clinical severity of sickle cell anemia (SCA). The major loci regulating HbF levels are HBB cluster, BCL11A, and HMIP-2 (HBS1L-MYB). However, the impact of noncoding single-nucleotide polymorphisms (SNPs) in these loci on clinical outcomes and their functional role on regulating HbF levels should be better elucidated. Therefore, we performed comprehensive association analyses of 14 noncoding SNPs in five loci with HbF levels and with clinical outcomes in a cohort of 250 children with SCA from Southeastern Brazil, and further performed functional annotation of these SNPs. We found SNPs independently associated with HbF levels: rs4671393 in BCL11A (β-coefficient = 0.28), rs9399137 in HMIP-2A (β-coefficient = 0.16), and rs4895441 in HMIP-2B (β-coefficient = 0.15). Patients carrying minor (HbF-boosting) alleles for rs1427407, rs93979137, rs4895441, rs9402686, and rs9494145 showed reduced count of reticulocytes (p < 0.01), while those carrying the T allele of rs9494145 showed lower white blood cell count (p = 0.002). Carriers of the minor allele for rs9402686 showed higher peripheral saturation of oxygen (p = 0.002). Patients carrying minor alleles in BCL11A showed lower risk of transfusion incidence rate ratio (IRR ≥ 1.3; p < 0.0001). This effect was independent of HbF effect (p = 0.005). Carriers of minor alleles for rs9399137 and rs9402686 showed lower risk of acute chest syndrome (IRR > 1.3; p ≤ 0.01). Carriers of the reference allele for rs4671393 showed lower risk of infections (IRR = 1.16; p = 0.01). In conclusion, patients carrying HbF-boosting alleles of BCL11A and HMIP-2 were associated with milder clinical phenotypes. Higher HbF concentration may underlie this effect.

Efficacy and toxicity of adjuvant chemotherapy on colorectal cancer patients: how much influence from the genetics?

We studied the predictive value for response and toxicity of functional polymorphisms in genes involved in the oxaliplatin/fluorouracil pathway in colorectal cancer patients. One hundred and twenty-seven (127) patients were treated with curative intended surgery followed by adjuvant chemotherapy with FOLFOX (fluorouracil, leucovorin and oxaliplatin) regimen. The median age was 65.53 (27–80) years (66.9% male, 59.1% rectum). The median follow-up was 8.5 years (IQR, 4.1–9.4). At the end of follow-up, 59 patients (46.5%) had relapsed or died in the whole study population. We did find that XRCC1GG genotype is associated with a higher risk of developing haematologic toxicity. Furthermore, we report a significant association of the TS 3′UTR 6 bp/6 bp polymorphism and the XRCC1 rs25487 with a higher risk of developing anaemia and diarrhoea, respectively. On the other hand, none of the studied polymorphisms showed clinically relevant association with disease-free survival and overall survival or early failure to adjuvant FOLFOX therapy.