A functional SNP in the 3′‐UTR of TAP2 gene interacts with microRNA hsa‐miR‐1270 to suppress the gene expression

The transporter associated with antigen processing 2 (TAP2) is involved in the development of multidrug resistance and the etiology of immunological diseases. In this study, we investigated whether the expression of TAP2 can be perturbed by single nucleotide polymorphisms (SNPs) located in 3′‐untranslated region (3′‐UTR) of the gene via interactions with microRNAs. Using a series of in silico assays, we selected the candidate microRNAs (miRNAs) with the potential to interact with functional SNPs of TAP2. The SNP rs241456—located in the 3′‐UTR of TAP2—resides in a potential binding site for hsa‐miR‐1270 and hsa‐miR‐620. HEK 293 cells, from a human kidney cell line, were used to characterize the extent of binding of miRNAs to each polymorphic allele of the SNP by a luciferase reporter gene assay. RNA electrophoretic mobility shift assays were used to evaluate the interaction between the miRNAs and each allele sequence of the SNP. We found that hsa‐miR‐1270 inhibited luciferase activity by binding to the T allele of the SNP in an allele‐specific manner. A negative correlation was also found between the expression of hsa‐miR‐1270 and the T allele of the SNP in kidney tissues. Our findings support the hypothesis that hsa‐miR‐1270 suppresses the production of TAP2 by binding to this SNP in the 3′‐UTR of this gene. Environ. Mol. Mutagen. 59:134–143, 2018. © 2017 Wiley Periodicals, Inc.     

Functional SNP in 3′‐UTR MicroRNA‐Binding Site of ZNF350 Confers Risk for Age‐Related Cataract

Many studies have suggested that individual susceptibility to age‐related cataract (ARC) may be associated with DNA sequence polymorphisms affecting gene regulation. As DNA repair is implicated in ARC pathogenesis and single‐nucleotide polymorphisms (SNPs) in the 3′‐terminal untranslated region (3′‐UTR) targeted by microRNAs (miRNAs) can alter the gene function, we hypothesize that the miRNA‐binding SNPs (miRSNPs) in DNA double‐strand break repair (DSBR) and nucleotide excision repair (NER) pathways might associate with ARC risk. We genotyped nine miRSNPs of eight genes in DSBR and NER pathways in Chinese population and found that ZNF350‐ rs2278414:G>A was significantly associated with ARC risk. Even though the Comet assay of cellular DNA damage indicated that all the subtypes of ARC patients had more DNA breaks in peripheral lymphocytes than the controls independent of rs2278414 genotypes, individuals carrying the variant A allele (AA and AG) had lower ZNF350 mRNA levels compared with individuals with GG genotype. Moreover, the in vitro experiment indicated that miR‐21‐3p and miR‐150‐5p specifically downregulated luciferase reporter expression in the cell lines transfected with rs2278414 A allele compared with rs2278414 G. These results suggested that the association of SNP rs2278414 with ARC might involve an altered miRNA regulation of ZNF350.     

Functional single nucleotide polymorphism in IL−17A 3′ untranslated region is targeted by miR‐4480 in vitro and may be associated with age‐related macular degeneration

Age‐related macular degeneration (AMD) is a leading cause of irreversible central vision loss in the elderly. Genetic factors contributing to AMD include single nucleotide polymorphisms (SNPs) in immune‐related genes including CFH, C2, CFI, C9, and C3, thus implicating these pathways in AMD pathogenesis. MicroRNAs (miRNAs) are powerful regulators of gene expression and execute this function by binding to the 3′ untranslated region (3′UTR) of target mRNAs, leading to mRNA degradation. In this study, we searched for the possible association of SNPs in the 3′UTR region of IL‐17A, a gene implicated in AMD pathogenesis without any previous SNP association with AMD. Using two independent sample cohorts of Caucasian subjects, six SNPs in the IL‐17A 3′‐UTR were selected for genotyping based on bioinformatic predictions of the SNP effect on microRNA binding. The SNP rs7747909 was found to be associated with AMD (P < 0.05) in the NEI cohort, using a dominant model logistic regression. Luciferase reporter gene assays and RNA electrophoretic mobility shift assays were performed using ARPE‐19 cells to confirm the preferential binding of microRNAs to the major allele of the SNP. Our findings support the hypothesis that microRNA‐mediated gene dysregulation may play a role in the pathogenesis of AMD. Environ. Mol. Mutagen. 57:58–64, 2016. © 2015 Wiley Periodicals, Inc.     

Irritable assault and variation in the COMT gene

Aggression is associated with the 'low' activity allele (Met) of the functional Val158Met polymorphism among people with schizophrenia spectrum disorders relative to the 'high' activity (Val) allele. We examined this polymorphism in a sample of 112 people with axis II personality disorders. Participants completed the Buss Durkee Hostility Inventory. Two single nucleotide polymorphisms in the COMT gene were genotyped in these participants classified as 'white' according to US Census Bureau definitions. We failed to observe an association between the Val158Met allele and aggression but observed an association between self-reported aggression and the G allele of a biallelic polymorphism located in the 3' UTR (rs16559). This allele is less prevalent among schizophrenics and is associated with lower COMT expression in the brain. These findings provide limited support for a role of COMT in modulating aggressive behavior, and are extended to people with personality disorders.     

Comprehensive evaluation of the genetic variants of interferon regulatory factor 5 (IRF5) reveals a novel 5 bp length polymorphism as strong risk factor for systemic lupus erythematosus

We analyzed a comprehensive set of single-nucleotide polymorphisms (SNPs) and length polymorphisms in the interferon regulatory factor 5 (IRF5) gene for their association with the autoimmune disease systemic lupus erythematosus (SLE) in 485 Swedish patients and 563 controls. We found 16 SNPs and two length polymorphisms that display association with SLE (P < 0.0005, OR > 1.4). Using a Bayesian model selection and averaging approach we identified parsimonious models with exactly two variants of IRF5 that are independently associated with SLE. The variants of IRF5 with the highest posterior probabilities (1.00 and 0.71, respectively) of being causal in SLE are a SNP (rs10488631) located 3' of IRF5, and a novel CGGGG insertion-deletion (indel) polymorphism located 64 bp upstream of the first untranslated exon (exon 1A) of IRF5. The CGGGG indel explains the association signal from multiple SNPs in the IRF5 gene, including rs2004640, rs10954213 and rs729302 previously considered to be causal variants in SLE. The CGGGG indel contains three or four repeats of the sequence CGGGG with the longer allele containing an additional SP1 binding site as the risk allele for SLE. Using electrophoretic mobility shift assays we show increased binding of protein to the risk allele of the CGGGG indel and using a minigene reporter assay we show increased expression of IRF5 mRNA from a promoter containing this allele. Increased expression of IRF5 protein was observed in peripheral blood mononuclear cells from SLE patients carrying the risk allele of the CGGGG indel. We have found that the same IRF5 allele also confers risk for inflammatory bowel diseases and multiple sclerosis, suggesting a general role for IRF5 in autoimmune diseases.     

Association of the serotonin transporter and 5HT1Dbeta receptor genes with extreme, persistent and pervasive aggressive behaviour in children

There is an inverse correlation between central nervous system serotonergic activity and human aggression, and aggressive traits are at least partially heritable. The present study sought to investigate the relationship between childhood aggression and polymorphisms of two serotonin system genes: the 5HT1Dbeta receptor gene and the serotonin transporter (5HTT) gene. Fifty children with a minimum 2-year history of aggression and scores above the 90th percentile on the Aggression subscales of both the Child Behaviour Checklist and the Teacher's Report Form were included in the study. All probands and locally recruited ethnically matched controls were genotyped for the 5HT1Dbeta G861C, 5HTTLPR (promoter) and 5HTT variable number of tandem repeats (VNTR) polymorphisms. Chi-square tests revealed a significantly reduced frequency of the 5HTT VNTR 10R allele in children displaying the high-aggression phenotype compared with normal controls (P=0.039). After correction for multiple comparisons, this association reached the level of a trend but was no longer significant. Probands also demonstrated an increased 5HT1Dbeta 861C allele frequency, but this was not statistically significant (P=0.156). 5HTTLPR was not found to be significantly associated with aggression, but our data support previous findings of an association between this polymorphism and attention deficit hyperactivity disorder (P=0.025). While these preliminary findings should be interpreted cautiously, our data suggest that the 5HTT VNTR polymorphism is associated with measures of aggressive behaviour in a sample of children displaying extreme, persistent and pervasive aggression.     

Minor histocompatibility antigens in Tunisians: could platelet endothelial cell adhesion molecule 1 marker be one of them?

Platelet endothelial cell adhesion molecule 1 (PECAM-1/CD31) is one of the human minor histocompatibility antigens that are the main targets of alloreactive T-cells after hematopoietic stem cells or solid organs transplantation. In order to investigate its polymorphism in Tunisians, three single nucleotide polymorphisms (SNPs) (rs668, rs12953 and rs1131012) were selected to perform an allele and haplotype analysis. Hundred-and-forty-two healthy and unrelated subjects were enrolled in this survey. Genomic DNAs were extracted using salting out method. SNP genotyping assays were performed with home-designed sequence-specific primers polymerase chain reaction (SSP-PCR). As a result, molecular analysis showed that PECAM-1 is one of the most polymorphic markers in the Tunisian population because minor allele frequency was 0.3, and minimum haplotype frequency was 0.03. A low linkage disequilibrium (D' = 0.45) between rs12953 and rs1131012 was noticed, although all other loci were in the Hardy-Weinberg equilibrium (minimum P value = 0.07). The frequencies were close to those reported in African-American and Caucasian groups.     

HLA-DQA13’-UTR序列多态性分析及microRNA的调控

目的 揭示HLA-DQAI基因3’-UTR区多态性的进化机制及其对基因表达的调控功能.方法 利用核苷酸变异率计算、系统发育树构建等群体遗传学分析方法将IMGT/HLA数据库中释放的20条HLA-DQAl全长序列多态性进行系统分析,揭示3’-UTR多态性的进化机制.利用miRanda vl.9软件提供的算法,对HLA-DQA1三种差异较大的3'UTR等位基因序列进行microRNA的靶位点预测,对分值较高的预测利用体外荧光细胞实验进行验证.结果 HLA-DQA1基因的3’-UTR具有极高的核苷酸变异率及跨物种多态性,表明其受到平衡选择的作用.预测出14种分值较高的microRNA-靶标复合 物,且14个microRNA与3种DQA1-3’-UTR等位基因靶标的结合自由能以及分值均有不同程度的差异.通过体外荧光表达实验证明,HLA-DQAl受到hsa-mir-658的负调控作用,且hsa-mir-658对DQAl-3’-UTR 3种等位基因特异性的结合对基因表达产生了影响.结论 HLA-DQAl基因表达水平受到microRNA的负调控,且HLA-DQA1 3’-UTR的多态性可影响与microRNA的结合而引起等位基因特异性表达.     

Aggression,Digit Ratio and Variation in Androgen Receptor and Monoamine Oxidase A Genes in Men

Variation in prenatal exposure to androgens is thought to be responsible for some of the individual differences in aggressive behavior among adults. A putative indicator of prenatal testosterone exposure, 2D:4D (the index to ring finger length) ratios have shown a weak correlation with aggression. Variation in sensitivity of the androgen receptor, resulting from polymorphism in the AR gene, is also thought to influence the relative expression of sexually dimorphic traits within each sex, including aggressive behavior and 2D:4D. Here we examine variation in aggression, 2D:4D, and polymorphism in the AR and MAO-A genes in a sample of 188 men. We find no evidence of AR gene influence on right hand 2D:4D, and a weak trend towards more feminine-typical left hand 2D:4D in men with more sensitive androgen receptors. Men with more sensitive androgen receptors tended to score lower on many of the subscales of the Aggression Questionnaire and Indirect Aggression Questionnaire. We found no influence of MAO-A allele on either digit ratio or aggressive behavior. We conclude that more masculine-typical 2D:4D does not reflect greater sensitivity to testosterone through variation in this locus on the AR gene, and that AR alleles conferring greater sensitivity to testosterone are associated with lower, not higher propensity to aggression.     

Association of polymorphism in MicroRNA 219‐1 with clearance of hepatitis B virus infection

Polymorphisms in the primary microRNA region may be associated with natural course of hepatitis B virus (HBV) infection. This study evaluated if the mircoRNA 219‐1 (miR‐219‐1) polymorphism can influence the susceptibility towards persistence of HBV infection and the progression to hepatocellular carcinoma (HCC) in patients with chronic HBV infection. A total of 1,439 individuals having either past or present evidence of HBV infection were enrolled for the study. The subjects were divided into four groups; (1) spontaneous recovery (n = 404), (2) chronic HBV carrier (n = 313), (3) chronic HBV carrier with cirrhosis (n = 305), and (4) hepatocellular carcinoma (n = 417). Genotyping was performed at three polymorphic variants (rs421446, rs107822, and rs213210) in the pri‐miRNA region of miR‐219‐1. The rs421446 T allele was found to be strongly associated with HBV clearance (OR = 0.73, P = 0.0005 in a codominant model and OR = 0.67, P = 0.0009 in a dominant model, OR = 0.69, P = 0.04 in a recessive model, respectively). The rs107822 G allele was also found to be associated with HBV clearance (OR = 0.79, P = 0.008 in a codominant model and OR = 0.72, P = 0.01 in a dominant model, respectively). In haplotype analysis, ht2 (T‐G‐T) and ht1 (C‐A‐C) were found to be in significant association with the clearance of HBV. However, no significant association was observed between miR‐219‐1 polymorphism and the risk of HCC occurrence. This result suggests that polymorphisms in the pri‐miRNA region of miR‐219‐1 might be a genetic factor for HBV clearance after infection. J. Med. Virol. 85:808–814, 2013. © 2013 Wiley Periodicals, Inc.     

CTLA-4基因多态性在重症肌无力发病机理中的作用

目的探讨细胞毒性T淋巴细胞相关抗原-4(cytotoxicTlymphocyteassociatedantigen-4,CTLA-4)基因第1外显子 49位点、启动区-318、-1661、-1772位点的多态性及其导致的无效转录对重症肌无力(myastheniagravis,MG)遗传易感性的影响。方法酶联免疫吸附实验测定MG患者和健康对照血清中可溶性CTLA-4的水平;限制性片段长度多态性分析检测第1外显子 49位点、启动区-318、-1661、-1772位点的多态性;转录因子核因子(nuclearfactor1,NF-1)和CCAAT/增强子结合蛋白β(CCAAT/enhancerbindingproteinbeta,c/EBPβ)结合位点通过染色质免疫沉淀实验得以验证。结果启动区-1772、-1661位点和第1外显子 49位点的多态性与MG,特别是伴发有胸腺瘤的MG密切相关。启动子-318位点的多态性与MG无关。CTLA-4基因4个多态性位点间有一个明确的正性连锁不平衡关系。MG患者血清可溶性CTLA-4的表达水平与等位基因的突变相关联。-1772、-1661位点的多态性可改变转录因子NF-1和c/EBPβ结合位点,而ConA、PHA则能促进NF-1和c/EBPβ的这种位点特异性转录活性。结论MG患者CTLA-4A/G 49、C/T-1772和A/G-1661多态性可导致无效转录,影响MG的遗传易感性,T→C-1772的突变能影响基因的剪接,从而干扰蛋白的表达和功能。