EGLN1基因两个位点多态性与藏族人群高原低氧适应的关系

目的 探讨西藏藏族人群EGLN1基因2个SNP(单核苷酸多态性)位点rs479200（C/T）、rs480902（T/C）多态性与高原低氧适应的相关性。
方法 选取世居西藏拉萨藏族150人及辽宁汉族150人的血样,提取白细胞基因组DNA,应用限制性片段长度多态性-聚合酶链反应（PCR-RFLP）技
术检测EGLN1基因2个SNP位点,分析其多态性特征。结果 rs479200位点等位基因C等位基因频率在藏族人和汉族人分别为71.33%和38.17%,
rs480902位点等位基因T等位基因频率在藏族人和汉族人分别为66.67%和36.67%,两组比较差异显著（P<0.01）;rs479200位点TT、TC和CC基因
型频率在藏族人和汉族人分别为6.67%和56.67%、29.33%和33.33%、64%和10%,rs480902位点TT、TC和CC基因型频率在藏族人和汉族人分别为
60.67%和9.33%、30.66%和28.67%、8.67%和62%。两位点TC基因型两组比较差异无统计学意义;TT和CC基因型两组比较差异均显著（P<0.01）。
结论 EGLN1基因rs479200（C/T）和rs480902（T/C）SNP位点多态性与西藏藏族适应高原低氧环境存在相关性。rs479200位点的CC基因型和
rs480902位点的TT基因型可能更有利于适应低氧环境。     

Common variants in DLG1 locus are associated with non‐syndromic cleft lip with or without cleft palate

Non‐syndromic cleft lip with or without cleft palate (nsCL/P) is a common craniofacial anomaly with a complex and heterogeneous aetiology. Knowledge regarding specific genetic factors underlying this birth defect is still not well understood. Therefore, we conducted an independent replication analysis for the top‐associated variants located within the DLG1 locus at chromosome 3q29, which was identified as a novel cleft‐susceptibility locus in our genome‐wide association study (GWAS). Mega‐analysis of the pooled individual data from the GWAS and replication study confirmed that common DLG1 variants are associated with the risk of nsCL/P. Two single nucleotide polymorphisms (SNPs), rs338217 and rs7649443, were statistically significant even at the genome‐wide level (P_trend = 9.70E?10 and P_trend = 8.96E?09, respectively). Three other SNPs, rs9826379, rs6805920 and rs6583202, reached a suggestive genome‐wide significance threshold (P_trend < 1.00E?05). The location of the strongest individual SNP in the intronic sequence of the gene encoding DLG1 antisense RNA suggests that the true causal variant implicated in the risk of nsCL/P may affect the DLG1 gene expression level rather than structure of the encoded protein. In conclusion, we identified a novel cleft‐susceptibility locus at chromosome 3q29 with a DLG1 as a novel candidate gene for this common craniofacial anomaly.     

Association of with‐no‐lysine kinase 1 and Serine/Threonine kinase 39 gene polymorphisms and haplotypes with essential hypertension in Tibetans

Tibetans have a higher essential hypertension prevalence compared with other ethnics in China. The reason might be due to their unique environmental influence, as well as genetic factor. However, limited studies focus on Tibetan genetics and its association with hypertension. The aim of this study was to investigate the association between With‐No‐Lysine (K) Kinase 1 (WNK1), Serine/Threonine kinase 39(STK39) genes variants and hypertension in the Tibetan population. 204 Tibetan hypertensive patients and 305 normotensive controls were recruited in an epidemiological survey conducted at 2 sites in the Ganzi Tibetan autonomous region. Patients were genotyped for nineteen WNK1 candidate tag single nucleotide polymorphisms (SNPs) and three STK39 SNPs, and haplotype analysis was performed. Results showed that the allele A in rs1468326 was overrepresented in hypertensive patients versus control (53.4% vs 42.9%, P < 0.05). The multivariable‐adjusted odds ratio (OR) for hypertension among CA + AA genotypes carriers was 1.60 (95% CI: 1.02–2.62, P < 0.05), and they also had a higher systolic blood pressure (136.5 ± 28.6 vs 131.7 ± 24.8 mmHg, P < 0.05). However, the TT genotype ratio in rs6749447 was lower in hypertensives (5.4% vs 10.8%, P < 0.05), and the hypertension risk for the TT genotype carriers in rs6749447 decreased after adjustment (OR 0.49, 95% CI 0.19–0.95, P < 0.05). Subjects with haplotype AGACAGGAATCGT showed 1.57 times higher risk of hypertension (95% CI 1.02–2.41, P < 0.05). In conclusion, SNP rs1468326 of WNK1, rs6749447 of STK39, and WNK1 haplotype AGACAGGAATCGT were associated with hypertension in Tibetan individuals. Environ. Mol. Mutagen. 59:151–160, 2018. © 2017 Wiley Periodicals, Inc.     

Genetic variants in RELN are associated with otosclerosis in a non‐European population from Tunisia

Otosclerosis is a common form of conductive hearing loss, caused by an abnormal bone remodelling in the otic capsule. Both environmental and genetic factors have been implicated in the etiology of this disease. A recent genome wide association study identified two regions associated with otosclerosis, one on chr7q22.1, located in the RELN gene, and one on chr11q13.1. A second study in four European populations has replicated the association of the RELN gene with otosclerosis. To investigate the association of these loci with otosclerosis in a non‐European population, we tested 11 SNPs from the two regions in 149 unrelated Tunisian patients and 152 controls. Four SNPs were significantly associated with otosclerosis. Three SNPs are located in the RELN region and the last one is located in the region on chromosome 11. We also observed a significant interaction with gender for rs3914132. This suggests an influence of sex on the association of RELN with otosclerosis. A meta‐analysis showed that the disease‐associated alleles in the Tunisian sample are the same as in all previously reported associations. Our study provides additional evidence implicating RELN in the development of otosclerosis. Additional functional studies should determine the role of RELN in the physiopathology of this disease.     

Polymorphisms at the SRBI locus are associated with lipoprotein levels in subjects with heterozygous familial hypercholesterolemia

Scavenger receptor, class B, type 1 (SRBI) is a promising candidate gene involved in the pathophysiology of atherosclerosis. We have examined the association of three common polymorphisms at the SRBI locus in 77 subjects who were heterozygous for familial hypercholesterolemia (FH). The alleles represented by polymorphisms in exon 1 and exon 8 were associated with variation in plasma concentrations of fasting triglyceride (TG). Mean plasma TG concentrations for homozygotes for the most common allele, and for heterozygotes and homozygotes for the less common allele were 85 +/- 6, 111 +/- 9 and 135 +/- 22 mg/dl (p = 0.011) for exon 1, and 96 +/- 11, 86 +/- 6 and 134 +/- 13 mg/dl (p = 0.007) for exon 8, after adjustment for age, sex and body mass index. In addition, the exon 8 polymorphism was associated with increased total cholesterol (320 +/- 15, 340 +/- 8 and 388 +/- 18 mg/dl, p = 0.015), very low density lipoprotein (VLDL) cholesterol (18 +/- 2.9, 15.7 +/- 1.6 and 33.4 +/- 3.9 mg/dl, p < 0.001) and low density lipoprotein (LDL) cholesterol (251 +/- 15, 270 +/- 8 and 312 +/- 10 mg/dl, p = 0.041) concentrations. In agreement with animal studies, our data also suggest a role for the SRBI in the metabolism of apolipoprotein B (apoB)-containing lipoproteins in humans. This pathway may constitute a backup mechanism to LDL receptor-mediated pathways for the catabolism of these lipoproteins, which could be particularly relevant in subjects with high levels of apoB-containing lipoproteins, such as those occurring in patients with FH.     

Association analysis of polymorphisms at the interleukin‐1 locus in essential hypertension

Infection with microorganisms such as Helicobacter pylori and Chlamidia pneumoniae has been associated with coronary heart disease (CAD) and hypertension (HT). Infection increases the release of pro‐inflammatory cytokines, thus facilitating interactions that lead to vascular damage and other effects. We hypothesized that genetically determined differences in activity or responsiveness of cytokine(s) might contribute to HT. The interleukin‐1 gene (IL1) cluster on chromosome 2q14 contains three related genes (IL1A, IL1B, and IL1RN) located within a 430‐kb region. These encode IL‐1α and IL‐1β, as well as their endogenous receptor antagonist, IL‐1ra. The IL1RN gene has a penta‐allelic 86‐bp tandem repeat in intron 2. Allele IL1RN* 2 is associated with a wide range of chronic inflammatory and autoimmune conditions, and its combination with the ? 31T variant of an IL1B C(? 31)T polymorphism constitutes a pro‐inflammatory haplotype that leads to vigorous IL‐1β production. We therefore tested each of these polymorphisms for association with HT. Subjects were white Anglo‐Celtic residents of Sydney, Australia. Frequencies of IL1B C(? 31)T genotypes CC, CT, and TT were 0.50, 0.40, and 0.10 in normotensive (NT) and 0.46, 0.46, and 0.08 in HT, respectively (χ² = 1.2, P = 0.55). T allele frequency in NT (0.30) was similar to that in HT (0.31). For the IL1RN variant, frequencies of alleles IL1RN* 1 and * 2 and combined minor alleles * 3, * 4, and * 5 were 0.61, 0.36, and 0.03 in NT and 0.54, 0.36, and 0.10 in HT, respectively (χ² = 11, P = 0.004). In conclusion, no association of the IL1B C(? 31)T with HT was found, whereas combined frequency of the minor alleles of the IL1RN polymorphism was increased in the HT cohort studied. © 2001 Wiley‐Liss, Inc.     

HIF1A基因两个位点多态性与夏尔巴人群高原低氧适应关系的研究

目的研究西藏高原夏尔巴人群缺氧诱导因子1α（hypoxia-inducible factor 1，alpha subunit；HIF1A）基因（HIF1A）第12外显子1772（C→T）、1790（G→A）多态性与高原低氧适应相关性。方法选取世居西藏高原夏尔巴族148人及广东汉族健康个体90人的血样，提取白细胞基因组DNA，聚合酶链反应-限制性片段长度多态性（polymerase chain reaction-restriction fragment length polymorphism，PCR-RFLP）检测HIF1A基因第12外显子1772（C→T）、1790（G→A）的单核苷酸多态性，分析其基因多态性特征。结果1772（C→T）CC、CT和TT基因型频率在夏尔巴人组与汉族对照组分别为14．19％和16．67％、39．19％和41．11％、46．62％和42．22％，两组间比较差异无统计学意义；1790（G→A）GG、GA和AA基因型频率在夏尔巴人组与汉族对照组分别为57．43％和75．56％、37．84％和21．11％、4．73％和3．33％，夏尔巴人组的GG基因型频率较汉族对照组的低（P〈0．01），而GA基因型频率高于汉族对照组（P〈0．01）。组合基因型分布，夏尔巴人CC＋GA、CT＋AA、TT＋GA和TT＋AA的组合基因型频率高于汉族组。结论HIFIA基因1790（G—A）多态性与夏尔巴人群高原低氧适应存在相关性，GA、AA基因型可能对低氧适应有利，值得进一步深入探讨。     

Polymorphisms at GLUT1 gene are not associated with the development of TSP/HAM in Brazilian HTLV‐1 infected individuals and the discovery of a new polymorphism at GLUT1 gene

The development of HTLV‐1 associated clinical manifestations, such as TSP/HAM and ATLL, occur in 2–4% of the infected population and it is still unclear why this infection remains asymptomatic in most infected carriers. Recently, it has been demonstrated that HTLV uses the Glucose transporter type 1 (GLUT1) to infect T‐CD4⁺ lymphocytes and that single nucleotide polymorphisms (SNP) in the GLUT1 gene are associated with diabetic nephropathy in patients with diabetes mellitus in different populations. These polymorphisms could contribute to a higher GLUT1 protein expression on cellular membrane, facilitating the entry of HTLV and its transmission cell by cell. This could result in a higher provirus load and consequently in the development of TSP/HAM. To evaluate the role of GLUT1 gene polymorphisms in the development of TSP/HAM in HTLV‐1 infected individuals, the g.22999G > T, g.15339T > C and c.‐2841A > T sites were analyzed by PCR/RFLP or sequencing in 244 infected individuals and 102 normal controls. The proviral load of the HTLV‐1 infected patients was also analyzed using Real Time Quantitative PCR. Genotypic and allelic frequencies of the three sites did not differ significantly between controls and HTLV‐1 infected individuals. There was no difference in genotypic and allelic distributions among patients as to the presence or absence of HTLV‐1 associated clinic manifestations. As regards the quantification of the provirus load, we observed a significant reduction in the asymptomatic individuals compared with the oligosymptomatic and TSP/HAM individuals. These results suggest that g.22999G > T, g.15339T > C, and c.‐2841A > T SNP do not contribute to HTLV‐1 infection nor to the genetic susceptibility of TSP/HAM in Brazilian HTLV‐1 infected individuals. J. Med. Virol. 81:552–557, 2009. © 2009 Wiley‐Liss, Inc.     

Analysis of inherited genetic variations at the UGT1 locus in the French‐Canadian population

The UDP‐glucuronosyltransferase UGT1 locus is composed of nine exon 1s, each flanked by a unique promoter region, and common exons (2, 3, 4, and the alternatively spliced exons 5a and 5b). Here, we characterized the genetic architecture of the UGT1 gene in a Caucasian sample. Overall, 98 variations in regulatory domains, exons and exon–intron boundaries were genotyped in 254 unrelated subjects, including 12 unreported UGT1 polymorphisms. We determined allele frequencies, computed pairwise linkage disequilibrium (LD), and inferred haplotypes; this thorough analysis yielding a limited number of common UGT1 haplotypes. Moreover, only 17 haplotype tagging single nucleotide polymorphisms (htSNPs) are required to capture most of the allelic diversity of the locus. Four haplotype blocks were inferred: Block 9/6 (UGT1A9, UGT1A7 and UGT1A6), Block 4 (UGT1A4), Block 3/1 (UGT1A3 and UGT1A1), and Block C (3′UTR). A high level of linkage exists between Blocks 9/6 and 3/1, while the 3′UTR SNPs are genetically isolated. The most common haplotype (16.5%) presents multiple deleterious alleles, mainly 1A1*28, 1A3*2, 1A6*2, and 1A7*4. More interestingly, we reveal the co‐occurrences of multiple deleterious variations, some of which could be associated with interindividual differences in glucuronidation. Comparison with the HapMap data set demonstrated differences in haplotypic diversity between ethnic samples, but similarity between Caucasian cohorts, as observed previously. This report provides relevant data for further pharmacogenomic studies. Hum Mutat 0, 1–12, 2009. © 2009 Wiley‐Liss, Inc.     

A susceptibility locus rs7099208 is associated with non-obstructive azoospermia via reduction in the expression of FAM160B1

Non-obstructive azoospermia (NOA) is a severe defect in male reproductive health that occurs in 1% of adult men. In a previous study, we identified that rs7099208 is located within the last intron of FAM160B1 at 10q25.3. In this study, we analysed expression Quantitative Trait Loci (eQTL) of FAM160B1, ABLIM1 and TRUB1, the three genes surrounding rs7099208. Only the expression level of FAM160B1 was reduced for the homozygous alternate genotype (GG) of rs7099208, but not for the homozygous reference or heterozygous genotypes. FAM160B1 is predominantly expressed in human testes, where it is found in spermatocytes and round spermatids. From 17 patients with NOA and five with obstructive azoospermia (OA), immunohistochemistry revealed that expression of FAM160B1 is reduced, or undetectable in NOA patients, but not in OA cases or normal men. We conclude that rs7099208 is associated with NOA via a reduction in the expression of FAM160B1.     

Sequence variants of the secreted phosphoprotein 1 gene are associated with total serum immunoglobulin E levels in a Japanese population

BACKGROUND: Secreted phosphoprotein 1 (SPP1) is a cytokine with pleiotrophic immunological activities, including activation of macrophage chemotaxis and T-helper type 1 (Th1) immune responses. SPP1 gene polymorphisms have been shown to be associated with several immune inflammatory diseases including multiple sclerosis (MS), which is characterized by fewer allergic symptoms and lower numbers of allergen sensitizations. OBJECTIVE: The present study examined whether SPP1 gene polymorphisms are associated with total serum IgE levels, atopy and asthma in a Japanese population. METHODS: This case-control association analysis examined 611 subjects, including 268 subjects with asthma. We genotyped three promoter and two exon polymorphisms at SPP1: -1687A/G; -381T/C; -94 deletion/G; 5891C/T; and 7052T/C. Results Association analyses of SPP1 polymorphisms showed that homozygosities for the 5891T allele (P=0.009) and 7052C allele (P=0.001) were significantly associated with increased levels of total IgE in non-asthmatic subjects. However, these variants were not associated with asthma and atopy. Interestingly, individuals carrying the 5891C allele, which is more prevalent in patients with MS in Japanese populations, displayed significantly lower levels of total serum IgE. Individuals homozygous for the 7052C allele, which is associated with development of systemic lupus erythematosus, displayed significantly higher total serum IgE levels. CONCLUSION: These findings suggest that genetic polymorphisms in SPP1 may play a role in controlling basal levels of total serum IgE, independent of atopy.     

Gene variants in PPARD and PPARGC1A are associated with timing of natural menopause in the general Japanese population

Objectives

Timing of menopause affects postmenopausal health risks. The objective of this study was to evaluate the associations of the single nucleotide polymorphisms (SNPs) in peroxisome proliferator-activated receptor (PPAR)-related genes (PPARD, PPARG, and PPARGC1A) and environmental factors with timing of natural menopause among the general Japanese population.

Study design

We analyzed cross-sectional data from 1758 women aged 40–69 years who were enrolled in the baseline surveys of the Japan Multi-institutional Collaborative Cohort (J-MICC) Study.

Main outcome measures

Associations of timing of natural menopause with its probable covariates and with target gene variants were evaluated by univariate and multivariate Cox proportional hazards models.

Results

Lower body mass index and later age at menarche were significantly associated with earlier natural menopause. Women with minor alleles at T-48444C in PPARD showed a significantly higher adjusted hazard ratio of 1.57 (95% confidence interval: 1.18–2.10) for earlier natural menopause. In contrast, women with minor alleles at Thr394Thr in PPARGC1A showed a significantly lower adjusted hazard ratio of 0.86 (0.76–0.97) for earlier natural menopause. These associations did not substantially alter when re-analyzed after excluding the subjects who self-reported a history of diabetes or the subjects whose age was more than 65 years.

Conclusions

Gene variants in PPARD and PPARGC1A might be associated with timing of natural menopause, probably through direct actions on the ovaries, among the general Japanese population.     

Common polymorphisms in the CTLA‐4 and CD28 genes at 2q33 are not associated with asthma or atopy

Recently, genetic linkage of the chromosomal region 2q33 with asthma has been shown. The genes coding for CD28 and CTLA‐4 have been localized to this chromosomal region. CD28 and CTLA‐4 have been shown to be involved as an important costimulatory signal in the regulation of allergic inflammation and TH2 cytokine production, and thus both genes are good candidate genes for asthma and atopy. Two common polymorphisms in the CTLA‐4 gene and one polymorphism in the CD28 gene found by single‐strand conformation polymorphisms (SSCP) analysis and direct genomic sequencing were tested for association with asthma and atopy phenotypes in a population of 260 largely atopic children and young adults. No association was found between any of the three polymorphisms and asthma or atopy phenotypes. The newly described common CD28 polymorphism is situated in the third intron of the gene. We conclude that neither gene is likely to exert a major influence on the development of asthma or atopy in our population. However, it might prove useful to test for association of these polymorphisms with asthma in populations recruited through asthmatic but not necessarily atopic individuals.