Gene Promoter Polymorphism Research Articles

Functional Genetic Variant in ATG5 Gene Promoter in Acute Myocardial Infarction.

Coronary artery disease (CAD) including acute myocardial infarction (AMI) is an inflammatory and metabolic disease mainly caused by atherosclerosis. Dysfunctional autophagy has been associated with abnormal lipid metabolism and inflammation. In previous studies, we have reported altered autophagic activity in AMI patients. As autophagy-related protein 5 (ATG5) is a core protein in autophagy, we speculated that altered ATG5 level may contribute to CAD and AMI development. In this study, the promoter of the ATG5 gene was genetically and functionally investigated in large groups of AMI patients (n = 378) and ethnic-matched healthy controls (n = 386). The results showed that a total of 15 genetic variants including 6 single-nucleotide polymorphisms (SNPs) in the ATG5 gene promoter were found in this study population. A novel deletion variant (g.106326168_70delTCT) and an SNP [g.106325757C > G (rs190825454)] were found in one 66-year-old male patient with non-ST-segment elevated AMI, but in none of controls. In cultured HEK-293 and H9c2 cells, the deletion variant significantly decreased the transcriptional activity of the ATG5 gene promoter (P < 0.01). In contrast, the genetic variants either identified only in controls or found in both AMI patients and controls did not affect the transcriptional activity of the ATG5 gene promoter (P > 0.05). Furthermore, an electrophoretic mobility shift assay showed that the deletion variant evidently affected the binding of a transcription factor. Therefore, the genetic variant identified in AMI may affect the activity of the ATG5 gene promoter and change the ATG5 level, contributing to AMI as a rare risk factor.

MHC Class II (DRB) Promoter Polymorphism and Its Role in Parasite Control among Malaria Patients.

MHC class II (MHCII) molecules are cell surface glycoproteins that play an important role to develop adaptive immune responses. MHCII-disease association is not restricted to structural variation alone but also may extend to genetic variations, which may modulate gene expression. The observed variations in class II gene expression make it possible that the association of MHCII polymorphism with diseases may relate to the level of gene expression in addition to the restriction of response to Ag. Understanding the extent of, and the mechanisms underlying, transcription factor DNA binding variation is therefore key to elucidate the molecular determinants of complex phenotypes. In this study, we investigated whether single nucleotide polymorphisms in MHCII-DRB regulatory gene may be associated with clinical outcomes of malaria in Plasmodium-infected individuals. To this end, we conducted a case-control study to compare patients who had mild malaria with those patients who had asymptomatic Plasmodium infection. It demonstrates that GTAT haplotype exerts an increased DRB transcriptional activity, resulting in higher DRB expression and subsequently perturbed Ag presentation and T cell activation, higher TLR-mediated innate immune gene expression, and Ag clearance, so low parasitemia in comparison with haplotypes other than GTAT (GTAC, GGGT). Hence, we hypothesized that DRB gene promoter polymorphism might lead to altered DRB gene expression, which could possibly affect the TLR-triggered innate immune responses in malaria patients. These genetic findings may contribute to the understanding of the pathogenesis of malaria and will facilitate the rational vaccine design for malaria.

Association of IL-10 gene promoter polymorphisms with susceptibility to pseudoexfoliation syndrome, pseudoexfoliative and primary open-angle glaucoma

BackgroundThe involvement of cytokines in pathogenesis of pseudoexfoliation syndrome and glaucoma has been demonstrated in several studies. The aim of the present study was to explore the association between three promoter polymorphisms −592C/A (rs1800872), − 819C/T (rs1800871) and -1082A/G (rs1800896) of interleukin 10 (IL-10) gene with susceptibility to pseudoexfoliation syndrome (PEX), pseudoexfoliative glaucoma (PEXG), and primary open-angle glaucoma (POAG).MethodsIn this study, 114 PEX, 118 PEXG, 114 POAG patients and 126 healthy individuals from Iranian population were participated. Detailed ophthalmic examinations by an ophthalmologist including slit-lamp bio-microscopic examination, dilated examination of the lens, gonioscopy, and funduscopy were carried out on patients and controls. Genomic DNA was extracted from the blood samples and ARMS–PCR was performed to detect promoter polymorphisms of IL-10.ResultsIn all three SNPs studied, there was a significant difference in the genotype distribution between patients and control subjects. Results revealed that the AA genotype of IL-10 -592C/A SNP is associated with PEX. However, TT genotype of −819C/T and AA genotype of -1082A/G SNP are significantly associated with susceptibility to either PEX or PEXG and POAG disorders. Furthermore, the ACC haplotype containing the IL-10 -1082A allele was associated with PEX (P = 0.02, OR = 5.76, 95% CI = 5.17–24.49), PEXG (P = 0.006, OR = 7.54, 95% CI = 6.62–30.76) and POAG (P = 0.003, OR = 8.11, 95% CI = 7.13–33.15).ConclusionsOur results demonstrated that IL-10 gene promoter polymorphisms are associated with susceptibility to PEX, PEXG and POAG in Iranian population. Considering the fact that IL-10 polymorphisms are associated with various IL-10 expressions, further research is needed to explain its involvement in these disorders and the formation of extracellular fibrillar amyloid deposits in PEX and PEXG.

Donor Heme Oxygenase-1 Promoter Gene Polymorphism Predicts Survival after Unrelated Bone Marrow Transplantation for High-Risk Patients.

Heme oxygenase-1 (HO-1), an intracellular enzyme that catalyzes the degradation of heme into biliverdin, free iron, and carbon monoxide, exerts anti-inflammatory and cytoprotective effects against endothelial cell injury. The HO-1 promoter gene has one important single-nucleotide polymorphism (SNP) rs2071746 (-413A>T) that is functional, and the A allele has been reported to be associated with higher HO-1 expression levels than the T allele. We investigated the influence of the HO-1 rs2071746 SNP on the transplant outcomes in 593 patients with hematological malignancies undergoing unrelated, human leukocyte antigen (HLA)-matched, T-cell-replete bone marrow transplantation (BMT) through the Japan Donor Marrow Program. In patients with high-risk diseases, the donor A/A or A/T genotype was associated with better 5 year overall survival (35% vs. 25%; p = 0.03) and 5 year disease-free survival (35% vs. 22%; p = 0.0072), compared to the donor T/T genotype. These effects were not observed in patients with low-risk diseases. The current findings therefore indicate that HO-1 rs2071746 genotyping could be useful for selecting donors and tailoring transplant strategies for patients with high-risk hematologic malignancies.

Regulatory SNP rs5743417 impairs constitutive expression of human β-defensin 1 and has high frequency in Africans and Afro-Americans.

The prediction of regulatory single nucleotide polymorphisms (rSNPs) in proximal promoters of disease-related genes could be a useful tool for personalized medicine in both patient stratification and customized therapy. Using our previously reported method of rSNPs prediction (currently a software called SNPClinic v.1.0) as well as with PredictSNP tool, we performed in silico prediction of regulatory SNPs in the antimicrobial peptide human β-defensin 1 gene in three human cell lines from 1,000 Genomes Project (1kGP), namely A549 (epithelial cell line), HL-60 (neutrophils) and TH 1 (lymphocytes). These predictions were run in a proximal pseudo-promoter comprising all common alleles on each polymorphic site according to the 1,000 Genomes Project data (1kGP: ALL). Plasmid vectors containing either the major or the minor allele of a putative rSNP rs5743417 (categorized as regulatory by SNPClinic and confirmed by PredictSNP) and a non-rSNP negative control were transfected to lung A549 human epithelial cell line. We assessed functionality of rSNPs by qPCR using the Pfaffl method. In A549 cells, minor allele of the SNP rs5743417 G→A showed a significant reduction in gene expression, diminishing DEFB1 transcription by 33% when compared with the G major allele (p-value=.03). SNP rs5743417 minor allele has high frequency in Gambians (8%, 1kGP population: GWD) and Afro-Americans (3.3%, 1kGP population: ASW). This SNP alters three transcription factors binding sites (TFBSs) comprising SREBP2 (sterols and haematopoietic pathways), CREB1 (cAMP, insulin and TNF pathways) and JUND (apoptosis, senescence and stress pathways) in the proximal promoter of DEFB1. Further in silico analysis reveals that this SNP also overlaps with GS1-24F4.2, a lincRNA gene complementary to the X Kell blood group related 5 (XKR5) mRNA. The potential clinical impact of the altered constitutive expression of DEFB1 caused by rSNP rs5743417 in DEFB1-associated diseases as tuberculosis, COPD, asthma, cystic fibrosis and cancer in African and Afro-American populations deserves further research.

Subjects with microvascular angina have longer GT repeats polymorphism in the haem oxygenase-1 gene promoter

Objective: Few studies have investigated haem oxygenase-1 gene (HMOX1) promoter polymorphism in microvascular angina (MVA).Materials and methods: HMOX1 promoter (GT)n repeats were examined in healthy controls (N = 220) and MVA subjects (N = 181).Results: The distribution of genotype of SS, SL and LL were significantly different in MVA (17%, 51%, 33%) vs. normal controls (35%, 46%, 20%) (p < 0.001, S allele: ≤30 repeats, L allele: >30 repeats). In multivariate analysis, carrier of L allele (odds ratio 2.772, p < 0.001) was a significant predictor for the diagnosis of MVA.Conclusions: Subjects with MVA had longer HMOX1 promoter (GT)n repeats than the healthy controls. Trial registration number: NCT01198730 at https://clinicaltrials.gov

Relationship Between Alcohol Dependence and Neuropeptide Y (NPY) Gene Promoter Polymorphisms in A Turkish Sample

Neuropeptide Y (NPY) is a protein widely expressed in the central nervous system and involved in diverse physiological processes, such as emotional regulation, nutritional behavior, and stress. In some populations, studies on alcohol dependence (AD) and the NPY gene have found that NPY variations increase alcohol consumption and thus may potentially be associated with AD. In this study, we investigated the relationship between NPY gene promoter polymorphisms and phenotypes related to alcohol use. A total of 417 male participants comprising 252 individuals with AD and 165 healthy individuals were included in this study and phenotypic data were collected. Polymerase chain reaction-restriction fragment length polymorphism (PCR/RFLP) and DNA sequencing METHODS were used for genotyping the rs16147 and rs17149106 polymorphisms in the promoter region of the NPY gene. The data of 384 participants were analysed to evaluate the possible relationship between genotypes and the diagnosis of AD, family history of AD, the severity of AD using the Michigan Alcoholism Screening Test (MAST), the age of onset of problematic alcohol use, the average amount of alcohol consumed per day for the last six months and the lifetime maximum alcohol consumption in one day. A significant difference was found between the AD and control groups concerning rs16147 polymorphism genotype distribution (p=0.025). No association with polymorphisms and alcohol-related phenotypes were demonstrated in the AD group. To our knowledge, this study shows for the first time in the literature that alcohol dependence is associated with NPY rs16147 polymorphism in the Turkish population.

Association of the sEH gene promoter polymorphisms and haplotypes with preeclampsia.

The epoxyeicosatrienoic acids (EETs) have antihypertensive, anti-inflammatory, and organ protective properties and their circulation levels are related to hypertension, diabetes mellitus, cardiovascular diseases, and preeclampsia. Soluble epoxide hydrolase (sEH) catalyses the degradation of EETs to less biologically active dihydroxyeicosatrienoic acids. Here, we sequenced the promoter region of EPHX2 to investigate the association between promoter sequence alterations that we thought to affect the expression levels of the enzyme and preeclampsia (PE). Nucleotide sequencing of the promoter region of the EPHX2, spanning from position -671 to +30, was performed on 100 pregnant women with PE and, 20 or more weeks pregnant normotensive, healthy women (n=100). Pregnant women who carry rs4149235, rs4149232, rs73227309, and rs62504268 polymorphisms have 4.4, 2.4, 2.3, and 2.8 times significantly increased risk of PE, respectively. CCGG (OR: 3.11; 95% CI: 1.12-8.62) and CCCA (OR: 0.45; 95% CI: 0.36-0.55) haplotypes were associated with an increased and decreased risk of PE, respectively. Four SNPs (rs4149232, rs4149235, rs73227309, and rs62504268) in the promoter region of the EPHX2, and CCGG and CCCA haplotypes of these 4 SNPs were significantly associated with PE. These SNPs in the promoter region may affect sEH expression and thus enzyme activity and may play a role in PE pathogenesis by causing individual differences in EET levels. However, future studies are needed to confirm our findings and examine the effect of these SNPs on the sEH expression and/or enzyme activity.

Interleukin-6 gene polymorhisms and interleukin-6 levels are associated with atherosclerosis in CKD patients.

Inflammation is a major risk factor for atherosclerosis. Genetic polymorphisms in the inflammatory cytokine genes have been associated with atherosclerosis. Because levels of inflammatory cytokines are markedly elevated in patients with chronic kidney disease (CKD), we hypothesized that genotypic variations in the interleukin-6 (IL-6) gene are a cause of systemic inflammatory states and atherosclerosis in South African CKD patients. 120 CKD patients and 40 healthy controls were included. Serum IL-6 and high-sensitivity C-reactive protein (hs-CRP) levels were measured. Functional polymorphisms in the IL-6 genes were genotyped using polymerase chain reaction-sequence specific primer (PCR-SSP) methods. Carotid intima-media thickness (CIMT) and the presence of plaque were assessed by B-mode ultrasonography. Serum IL-6 and hs-CRP levels were increased in patients with CKD compared with healthy controls (p < 0.001). In CKD patients, serum IL-6 above the median value was associated with carotid plaque (OR: 2.11; 95% CI: 1.74-2.57, p=0.004), with excess risk confined to the group with high IL-6 levels. Significant associations were found between the IL-6 gene and atherosclerosis in the CKD group (for G/G genotype: OR=1.21, 95% CI=1.05-1.39, p=0.012; for GG+GC vs. CC: OR=1.14, 95% CI=1.02-1.28, p=0.035). Patients with GG+GC genotype of the IL-6 gene polymorphism had higher levels of IL-6 than those with CC genotype (p=0.029). In South African CKD patients, the IL-6 gene promoter polymorphism is associated with high serum IL-6 levels and atherosclerosis. The relationship between atherosclerosis and -174G/C polymorphism in the IL-6 gene suggests that IL-6 may be a potential pro-inflammatory mediator of atherosclerosis in CKD patients.

Association of GCK Gene Promoter Polymorphism and their Role in its mRNA Expression among Type 2 Diabetes Mellitus Patients

Introduction: Glucokinase (GCK) gene alteration or inactivation leads to Maturity-Onset Diabetes of the Young (MODY) and Neonatal Diabetes. Alterations in GCK gene has been shown to be associated with increased risk of type 2 diabetes, hyperglycaemia and impaired beta cell function. Aim: To evaluate the GCK (-30G/A, rs1799884) alterations in Type 2 Diabetes Mellitus (T2DM) patients. Materials and Methods: After patients’ selection, blood samples were taken and all biochemical parameters were analysed by auto-analyser using serum. Whole blood samples were used to extract DNA and RNA for genotyping of -30G/A polymorphism using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) as well as GCKmRNA expression using quantitative real time PCR. Results: Several parameters such as fasting sugar, serum uric acid, Low Density Lipoprotein (LDL), High Density Lipoprotein (HDL), Triglyceride (TG), Cholesterol, high-sensitivity C-Reactive Protein (hs-CRP) were analysed among T2DM cases and healthy controls and differences among them were found to be significantly associated (p&lt;0.0001). It was observed that patients who were smoking among T2DM cases, were found to be associated with increased fasting sugar (p=0.001), postprandial sugar (p&lt;0.0001), HbA1c (p=0.003), blood urea (p=0.01), cholesterol (p=0.02) compared to those who were not smokers. T2DM patients who were alcoholic, showed increased LDL (p=0.006) and cholesterol (p=0.01) compared to non-alcoholic T2DM patients. T2DM cases which were reported hypertensive, showed increased hs-CRP (p=0.02) and cholesterol (p=0.02), compared to non-hypertensive T2DM cases and differences among them were found to be significantly associated. Significant differences were observed in distribution of GCK -30G/A genotypes among T2DM cases and healthy controls (p&lt;0.0001). Odds ratio was calculated and it was observed that the heterozygous GA genotype had 4.66 odds ratio while odds ratio for mutant AA genotype was 35.98 in reference to wild type. Patients with homozygous GG showed 0.25 mean fold decreased GCK mRNA expression while heterozygous GA and mutant AA genotype showed more than 0.17 and 0.16 fold decreased. GCK mRNA was observed and differences among them was found to be significant (p&lt;0.0001). Conclusion: Study revealed that GCK heterozygous GA and mutant AA genotypes were associated with T2DM risk and decreased expression may be responsible for disease progression and worsening of the disease.

Increased potassium excretion in children with monosymptomatic nocturnal enuresis: could it be related to Kir 4.1- KCNJ10 gene polymorphism?

There are controversial results in the literature regarding urinary electrolytes, especially potassium, in enuretic children. KCNJ10 channel protein, a member of the Kir 4.1 family is expressed in renal distal tubules and has an important function in renal ion transport. We investigated whether KCNJ10 gene polymorphisms are associated with clinical and laboratory findings of a group of Turkish children with monosymptomatic primary nocturnal enuresis (MNE). Ninety-seven MNE children and 100 healthy controls were tested for three single nucleotide polymorphisms (SNPs) in the KCNJ10 gene. The transversions in SNPs were G to A for intron 1(SNP1), G to A for exon 2 (SNP2), and T to C transition for promoter (SNP3). All SNPs were genotyped by PCR-restriction fragment length polymorphism. SNP3 in promoter of KCNJ10 gene showed strong association with MNE children for distribution of genotype and allele frequency, while SNP1 in intron 1 and SNP2 in exon 2 were noninformative. The distribution of TT, TC, and CC genotypes for SNP3 was 66%, 26.8% and 7.2% respectively in MNE compared with 38%, 59% and 3% respectively in controls (p < 0.0001). In enuretic children, TT genotype was higher and there was an increased potassium excretion in children with TT genotype (P < 0.05). We conclude that KCNJ10 gene promoter polymorphism may have a role on potassium excretion in Turkish MNE children. This is the first study in literature evaluating KCNJ10 gene polymorphism in this patient population. Future studies investigating the other SNPs, mutations or altered regulation of Kir4.1 in larger samples would help clarify the role (s) of KCNJ10 gene in enuresis.

THE EFFECT OF MUSCLE DAMAGE AND THE IL-6-174C/G POLYMORPHISM ON THE SERUM IL-6 LEVELS OF OLDER MEN

ABSTRACT Introduction Fast population aging is a global reality. Today’s major challenge is to promote the healthy aging of more and more people by acting on factors that can be modified, such as physical exercise. Regular exercise could contribute to the prevention of chronic diseases associated with aging. Research has been conducted on the physical training response of elderly individuals, but there is not yet any consensus on the influence of strength training or IL-6 polymorphism on levels of inflammatory markers such as IL-6 and muscle damage marker CK, particularly in healthy elderly male individuals. Objectives The aim of this study was to evaluate the relationship of IL-6 promoter -174 C/G gene polymorphism on systemic IL-6 responses and muscle damage after eccentric strength training in elderly men. Methods This is a prospective, high-quality study. Gene frequency of polymorphism of promoter gene IL6 G-174C was identified using the Hardy-Weinberg test in 28 older male volunteers. The relationships of each genotype with IL-6 and CK serum levels were analyzed. CK and IL-6 levels were determined at pre-training and 0h, 3h, 24h, and 48h post-training periods. Results Differences in baseline and post-training IL-6 levels of genotypic groups were observed for all time periods analyzed (p = 0.029). Eccentric exercise efficiently reduced post-intervention muscle damage, thus showing a statistical difference between the pre- and post-intervention time points ( p = &lt;0.0005). Conclusion Eccentric training influenced CK and IL-6 modulation independently of the polymorphism of the IL-6 promoter gene -174 C/G. Level of evidence II, Prospective comparative type.

Impact of IL-18 gene promoter polymorphisms on renal cell carcinoma occurrence and prognosis in Chinese Han population*

Abstract Objective Genetic polymorphisms in various inflammatory cytokines have been associated with the risk and growth or invasiveness of renal cell carcinoma (RCC). However, the molecular basis of RCC pathogenesis is unclear. The aim of this study was to explore a possible association between two IL-18 gene promoter polymorphisms, -137G/C and -607C/A, and RCC occurrence and prognosis in a Chinese Han population. Methods Chinese Han patients with RCC (n = 175) and age-matched healthy controls (n = 200) were analyzed by single nucleotide polymorphism genotyping during follow-up. Results IL-18-137G allele frequency was significantly higher in patients with lymph node metastasis (Odds ratio [OR], 3.52; 95% confidence interval [CI], 0.97-16.17; P = 0.045). The IL-18-607 CC genotype was associated with distant metastasis (OR, 2.81; 95% CI, 1.35-6.24; P = 0.025). The IL-18-137 G allele was correlated with more advanced tumor stage (OR, 1.83; 95% CI, 1.05-3.72; P = 0.026) and higher tumor grade (OR, 2.23; 95% CI, 0.78-4.12; P = 0.041). The IL-18-607 CC genotype frequency was significantly higher in patients with more advanced cancer stage (OR, 2.92; 95% CI, 1.80-6.87; P = 0.001) and higher tumor grade (OR, 2.21; 95% CI, 1.25-12.25; P = 0.035). The IL-18-607 allele was associated with more advanced cancer stage (OR, 2.47; 95% CI, 1.38-3.83; P = 0.002).Carriers of the GG genotype with the -137G/ C polymorphism had a 2.165-times higher risk of RCC progression than carriers of the GC genotype (Hazard ratio = 2.15, 95% CI, 1.270-3.687). Conclusion The IL-18-137 G allele was correlated with more advanced stage, higher tumor grade, and lymph node metastasis. IL-18 gene promoter polymorphism -137G/C may thus influence the prognosis of RCC patients.

Relationship between polymorphisms in -572G/C interleukin 6 promoter gene polymorphisms (rs1800796) and risk of rheumatoid arthritis: A meta-analysis.

This meta-analysis was aimed to investigate the association between -572G/C interleukin (IL)-6 gene polymorphism and occurrence risk of rheumatoid arthritis (RA). Literature search was conducted in PubMed, Embase, Springer and Google Scholar up to November 2018. The pooled odds ratios (ORs) and 95% confidence interval (CI) were calculated by Revman 5.3. A total of six case-control studies were included in this meta-analysis. In the allele model (G vs C), homozygous gene model (GG vs CC), recessive gene model (GG vs GC+CC), and dominant gene model (GG+GC vs CC), the pooled estimate indicated there was significant association between -572G/C IL-6 gene polymorphism and risk of RA. However, no significant statistical results were found in meta-analyses of heterozygote gene models. The -572G/C IL-6 gene polymorphism is associated with the risk of RA. The GG genotype may be the main contributor in increasing susceptibility to RA.

Association of MMP-1 (rs1799750)-1607 2G/2G and MMP-3 (rs3025058)-1612 6A/6A Genotypes With Coronary Artery Disease Risk Among Iranian Turks.

The study was conducted to evaluate the association between MMP-1 (rs1799750)-1607 1G/2G and MMP-3 (rs3025058)-1612 5A/6A polymorphisms/haplotypes and coronary artery disease (CAD) risk among Iranian Turks. Totally, 102 patients with CAD and 102 healthy subjects joined the study. Genomic DNA isolation was carried out using "salting out" method from 3 to 4 mL of whole blood samples. The MMP-1 (-1607 2G/1G) and MMP-3 (-1612 5A/6A) promoter gene polymorphisms were detected via polymerase chain reaction restriction fragment length polymorphism. Our results indicated that the frequencies of the MMP-1 (-1607) 2G alleles and 2G/2G genotypes and the MMP-3 (-1612) 6A alleles and 6A/6A genotypes were higher in CAD patients older than 50 years than in healthy controls (P < 0.05). We failed to show statistically significant differences between the CAD patients younger than 50 years and controls concerning MMP-1 -1607 ins/delG (1G > 2 G, rs1799750) and MMP-3 -1612 ins/delA (5A/6A, rs3025058) polymorphisms (P > 0.05). The frequencies of MMP-3/MMP-1 haplotypes were not statistically different among tested groups (P > 0.05). This examination, as the first study of its own kind in Iranian Turks, reported association between MMP-1 (rs1799750) -1607 2G/2G and MMP-3 (rs3025058) -1612 6A/6A genotypes and CAD risk in patients older than 50 years.

Uridine diphosphate glucuronosyl transferase 1A (UGT1A1) promoter polymorphism in young patients with sickle cell anaemia: report of the first cohort study from Nigeria

Background(TA) n repeat sequence (rs8175347) of UGT1A1 gene promoter polymorphism is associated with serum bilirubin levels and gallstones among different sickle cell anaemia (SCA) populations. There are no data on UGT1A1 polymorphisms and their impact on Nigerian SCA patients. In this study, we determined the distribution of the UGT1A1 (TA) n genotypes among a group of young Nigerian SCA patients and healthy controls. In addition, the influence of UGT1A1 (TA) n genotypes on the laboratory and clinical events among the patients was determined.MethodsThe distribution of the UGT1A1 (TA) n genotypes among 101 young Nigerian SCA patients and 64 normal appropriate controls were determined and studied. The UGT1A1 (TA) n genotypes were further classified into subgroups and used to differentiate the clinical events and laboratory parameters of the patients.ResultsFour (TA) n alleles:(TA)5, 6, 7, and 8 were found. These were associated with 10 genotypes: TA5/5, 5/6, 5/7, 5/8, 6/6, 6/7, 6/8, 7/7, 7/8, 8/8. The normal (wild-type)-(TA) 6/6), low- (TA) 7/7, 7/8, 8/8), intermediate- (TA) 5/7, 5/8, 6/7, 6/8), and high-activity (TA) 5/5, 5/6,) genotypes were found in 24.8, 24.8, 41.5, and 8.9% patients and 20.3, 15.6, 61, and 3.1% controls respectively. The general genotype distribution of the patients and control group were not significantly different. There were significant differences in serum bilirubin and lactate dehydrogenase (LDH) of the patients when differentiated by the UGT1A1 (TA) n genotypes (p<0.05). Asymptomatic gallstones were found in 5.9% of patients and were significantly of the low-activity genotypes sub-group 5 (20%) vs 1(1.3%) p = 0.0033. Although, bilirubin and fetal hemoglobin (HbF) of patients with gallstones were significantly different from those without gallstone, only the serum bilirubin was associated with UGT1A1 (TA) n genotypes on multivariate analysis (p < 0.0001).ConclusionThis study highlights the contribution of UGT1A1 polymorphisms, a non-globin genetic factor, to the laboratory and clinical manifestations of young Nigerian SCA patients for the first time. It also shows that children with co-inheritance of low UGT1A1 (TA) n affinity genotypes may be at risk of gallstone, hence the need to follow them up.

Polymorphisms of the Chicken Mx Gene Promoter and Association with Chicken Embryos' Susceptibility to Virulent Newcastle Disease Virus Challenge.

Newcastle disease is a devastating viral disease of chicken in low- and middle-income countries where the backyard production system is predominant. Marker-assisted selection of chickens that are resistant to Newcastle disease virus (NDV) is the promising strategy that needs to be explored. The aim of the present study was to investigate polymorphisms of the promoter region of the chicken Mx gene and association with Kuroiler, Sasso, and local Tanzanian chicken embryos' survival variability to virulent NDV infection. Chicken embryos were initially challenged with a minimum lethal dose of virulent NDV suspension and then were followed over time to gather information on their survival variability. Using the survival data, high and less susceptible cohorts were established, and a total of 88 DNA samples from high and less susceptible groups were genotypes by sequencing. Five single-nucleotide polymorphisms (SNPs), which were previously reported, were detected. Interestingly, for the first time, the findings demonstrated the association of the promoter region of chicken myxovirus-resistance (Mx) gene polymorphisms with chicken embryos' susceptibility to the virulent NDV challenge. At the genotypic level, the SNP4 G > A mutation that was located within the IFN-stimulating response element was associated (LR: 6.97, P=0.03) with chicken embryos' susceptibility to the virulent NDV challenge. An allele G frequency was higher in the less susceptible cohort, whereas an allele A frequency was higher in the high susceptible cohort. At the haplotype level, the haplotype group ACGC was associated (OR: 9.8, 95% CI: 1.06–79.43, P=0.042) with the same trait and had a resistant effect. In conclusion, the results have demonstrated the association of chicken Mx gene promoter polymorphisms and chicken embryos' survival variability to the virulent NDV challenge, and the information is useful for breeding programs designed to develop chicken genotypes that are resistant to Newcastle disease virus.

The role of two common FOXP3 gene promoter polymorphisms in preeclampsia in a Turkish population: a case–control study

Preeclampsia (PE), which occurs in approximately 5% of pregnancies worldwide and constitutes clinically serious complications in 2–3%, is one of the leading causes of maternal and prenatal morbidity and mortality. Recent studies report that regulatory T (Treg) cells, which act as immunosuppressant, are associated with PE. It is clearly defined that FOXP3/Scurfin (Forkhead Box P3) is involved in the development and function of Tregs. However, there are different conclusions regarding the relationship between PE and FOXP3 gene polymorphisms for different populations. For this reason, in this study we investigate the association between FOXP3 gene promoter region polymorphisms and PE in a Turkish population 500 PE patients and 500 healthy pregnant women. Blood samples taken from pregnant women were studied by PCR-RFLP method. As a result, rs2232365 polymorphism was significantly associated with disease (p < .0001) while no significant association was found between rs3761548 polymorphism and the disease (p = .17). Based on these results, it is though that FOXP3 rs2232365 polymorphism may be predisposed to PE development in terms of Turkish population. However, further and functional studies are needed in terms of other polymorphisms and mutations.IMPACT STATEMENTWhat is already known on this subject? A number of recent publications suggest that Tregs may play a role in the pathogenesis of PE. It is known that a stable and high FOXP3 expression is required to maintain the suppressive T cell function of Tregs. Down regulation of FOXP3 in PE has been reported in many previous studies, but the mechanism is still uncertain.What do the results of this study add? Our study has examined two FOXP3 promoter region polymorphisms in terms of Turkish population for the first time. Rs2232365 polymorphism associated with the disease in heterozygous genotype.What are the implications of these findings for clinical practice and/or further research? It has been shown that FOXP3 gene promoter region polymorphisms may be associated with PE for Turkish population. Our results can be a guide for more detailed statistical evaluations and functional studies.

Genetic diversity of CD14, CD28, CTLA-4 and ICOS gene promoter polymorphism in African and American sickle cell disease

Variable immune response to external stimuli remains a major concern in sickle cell disease (SCD), with such responses predicted to be contributors to disease pathogenesis. Elucidating the diversity of host genes contributing to immune response would assist to clarify differing outcomes among and between disease groups. We hypothesize that there is a significant interethnic diversity in the CD14 (rs2569190), CD28 (rs35593994), CTLA-4 (rs5742909) and ICOS (rs4404254) gene polymorphisms among and between SCD groups. We genotyped single nucleotide polymorphisms of the 4 loci among African and African American SCD and control groups and between SCD groups. In all, 375 individuals from Mali (145 SCD and 230 controls) and 700 DNA samples from the United States (321 SCD and 379 controls) were subjected to a PCR-RFLP assay. We found no intraethnic difference in genotypic and allelic frequencies of the 4 loci among Africans and African Americans, potentially significant in disease association studies, including a similar observation for interethnic frequencies of CD28, CTLA-4 and ICOS genes, but not CD14. The CD14 (rs2569190) gene promoter demonstrated a significant difference (p < 0.02) between African and African American SCD groups, with the mutant variant (−159 T/T) more frequent (p < 0.0002) in African American SCD (38.9% versus 26.2%). The higher frequency of CD14 mutants among African Americans without an accompanying defect in CD28, CTLA-4 and ICOS diversity possibly indicates a defective innate response, driven by CD14, is untethered to downstream T cell differentiation or effector function. Additionally, we show that CD28 (rs35593994) mutant variants have no impact on T cell differentiation, as the ICOS gene provides an alternative pathway to override this impairment. We conclude that in spite of the defect in CD14, T cell selection and differentiation is unimpeded and a robust adaptive immune response initiated.

PD-L1 gene copy number and promoter polymorphisms regulate PD-L1 expression in tumor cells of non-small cell lung cancer patients

Most drugs targeting PD-1 or PD-L1 are more effective when cancer cells of non-small cell lung cancer (NSCLC) patients express PD-L1 protein. The polymorphisms of PD-L1 gene and PD-L1 gene copy number could be responsible for PD-L1 mRNA and protein expression.We analyzed PD-L1 protein expression using two IHC assays, mRNA (PD-L1) expression by qRT-PCR, PD-L1 gene promoter region polymorphisms (rs822335 and rs822336) by qPCR and PD-L1 gene copy number by fluorescence in situ hybridization method.Patients with CC genotype in rs822335 had significantly (p = 0.043) higher percentage of tumor cells with PD-L1 expression (test with 22C3 antibody) than patients with CT or TT genotypes. PD-L1 gene copy number significantly positively correlated with percentage of tumor cells with PD-L1 expression detected in tests with 22C3 antibody (p = 0.005, R = +0.442) and with SP142 antibody (p = 0.021, R = +0.369). PD-L1 gene copy number did not correlate with PD-L1 mRNA expression. Patients with PD-L1 expression tested with 22C3 antibody had significantly higher expression of PD-L1 mRNA (p = 0.023), number of chromsosme 9 centromeres (p = 0.023) and PD-L1 gene copy number (p = 0.003) than patients without PD-L1 expression on tumor cellsPD-L1 gene polymorphisms and PD-L1 gene copy number may be a predictor for PD-L1 protein expression on tumor cells.